Dear NEST Users & Developers,
we're currently working on a custom OpenMPI BTL (supporting a custom
FPGA-based NIC) at the National Institute for Nuclear Physics in Rome,
Italy and we have an error when running hpc_benchmark(this test is
currently used as simple validation test) with 2 processes (one on each
of 2 hosts), the command we run is like:
mpirun -n 2 -H host1:1,host2:1 --bynode --report-bindings -mca btl
apelink,self,sm python hpc_benchmark.py (apelink is our custom BTL
component)
but then we see this error:
python:
[...]/NEST_with_local_ompi/nest-simulator-3.6/nestkernel/target_table.cpp:107:
void nest::TargetTable::add_target(size_t, size_t, const
nest::TargetData&): Assertion `syn_id < secondary_send_buffer_pos_[ tid
][ lid ].size()' failed. [host:23979] *** Process received signal ***
[host:23979] Signal: Aborted (6) [host:23979] Signal code: (-6)
My guess is that we are transferring something incorrectly (maybe during
the initialization/setup phase?), but I'm not sure what the assert
expects to have in secondary_send_buffer_pos_[ tid ][ lid ].size() and
how this field should be set.
Best,
Michele
Dear NEST Users & Developers!
I would like to invite you to our next fortnightly Open NEST Developer Video Conference today
*Monday January 29, 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 bunch of topics that came up and that were 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
o Changed Model registration for NEST Models (from last meeting)
o Proposed new model with an approximation for nonlinear NMDA receptors (#2979 <https://github.com/nest/nest-simulator/pull/2979>)
o Proposed multi-state models (#3069 <https://github.com/nest/nest-simulator/pull/3069>)
o Report from LASCON IX
The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2024-01-29-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-01-29-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
----------------------------------------------------------------------
I'm using Google Bard's Gemini to learn NESTML. It's giving me some
unexpected results:
import nestml
from nestml.network import Network
from nestml.models import ConeNakaRushton
# Define network with Naka-Rushton cone model for primate 'cone_type' cones
network = Network()
cone_population = network.add_population("cones", ConeNakaRushton(species=
"human", cone_type=cone_type))
The NESTML network and models packages don't seem to exist. Also, how do I
find more information about the network and models packages (or packages in
general) for NESTML?
--
Alvin J. Spivey, Ph.D.
(c) 843.267.8055
Dear NEST Users & Developers!
🎈🎉🎈 Happy New Year! 🎈🎊🎈
I would like to invite you to our first fortnightly Open NEST Developer Video Conference in 2024, today
*Monday January 15, 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/2024-01-15-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-01-15-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 of Neuroscience and Medicine
Computational and Systems Neuroscience (INM-6) &
Institute for Advanced Simulation (IAS-6)
Theoretical Neuroscience & JARA (INM-10)
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 Colleagues,
The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NEST Simulator to the NEST Conference 2024.
Save the date for the virtual conference taking place on June 17–18, 2024!
The annual NEST Conference provides an opportunity for the NEST Community to meet, exchange success stories, swap advice, learn about current developments in and around NEST spiking network simulation and its application. We particularly encourage young scientists to participate in the conference!
Registration and abstract submission will open early next year. For more information on the event please visit the conference website
https://nest-simulator.org/conference.
We are looking forward to seeing you in June and wish you happy holidays and a good start into the new year!
Hans Ekkehard Plesser and colleagues
[Image]
--
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 All, I am going to add weights for excitatory and inhibitory synaptic currents according to this equation:
can you help me how I can add S(Wji) to a simple neuron model like one I attached to this email?Thanks and BR, Atiyeh
Dear all!
Due to an on-site Hackathon today, we will not have a NEST Open Developer VC.
See you on 18 December for the final VC of the year!
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 colleagues,
We are procuring a new small computing cluster on which we want to primarily run NEST simulations.
Our models are medium in size (100s of thousands of neurons) but we run them for relatively long biological times (100s of seconds), so the network setup duration is mostly irrelevant for us.
What we would like to ask is if there is any insight into the current NEST simulator in terms of what are the hardware bottlenecks of these types of simulations. Are we going to do better with investing into more cores or higher clock speeds or more cache, or faster RAM? I understand that this is a complex multi-factor optimization question, but any insights or links to existing material that would
allow us to form an informed decision would be greatly appreciated.
Best regards,
Remy Cagnol.
Dear NEST Users!
I am happy to report that I have successfully built NEST with Python 3.12. Right now, there are just one little problem: Unittest.assertDictContainsSubset() has been removed in Python 3.12, so five tests fail currently. This is fixed by https://github.com/nest/nest-simulator/pull/2997.
Best regards,
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
