Dear NEST Users,
I have just published a paper in Frontiers in Neuroinformatics
Plesser HE (2024)
Commentary: Accelerating spiking neural network simulations with PymoNNto and PymoNNtorch.
Front. Neuroinform. 18:1446620. doi: 10.3389/fninf.2024.1446620
confirming that NEST/NESTML provide correct simulations. I just wanted to let you know about this result because a paper earlier this year had included a figure showing that NEST got different results than several other simulators. It turned out that exact integration is exact as the name says, while forward Euler is not.
Best,
Hans Ekkehard
--
Prof. Dr. Hans Ekkehard Plesser
Research Committee Chair, Faculty of Science and Technology
Head, Department of Data Science
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,
We would like to inquire your interest in Application-Oriented Hackathons, and are thus reaching out to you with this survey:
https://ictsurvey.helmholtz-muenchen.de/index.php?r=survey/index&sid=234889…
which will be active till 25 October, 2024.
For now, we plan to organize two such hackathons:
1. in Aachen, Germany in the week 9-13 December, 2024
2. in Aas, Norway in the week 23-27 June, 2025
These in-person events would allow you to bring your ideas for new NEST features and get started implementing them with the help of experienced NEST developers.
Please note that your participation would be at your own expense.
We look forward to your feedback!
Best wishes,
Susanne Kunkel
on behalf of NEST Initiative
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
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
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Dear NEST Users & Developers!
I would like to invite you to our next fortnightly Open NEST Developer Video Conference today
*Monday October 21, at 11:30 CEST (UTC+0200).*
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/2024-10-21-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-10-21-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
----------------------------------------------------------------------
Hi all!
What I'm doing:
I've used v2.20.2 on HPC (bwForCluster NEMO) for my large-scale simulations involving structural plasticity. Now I'm trying to move to v3.8.
How am I doing this?
I built NESTv3.8 on my HPC workspace following the cmake instructions mentioned at: https://nest-simulator.readthedocs.io/en/v3.8/installation/cmake_options.ht…
Here's an overview of my build and installation commands:
```
source /<some_path>/NESTv3.8/bin/activate # activate a fresh python venv (v3.9.7) [optional]
module load mpi/openmpi/4.0-gnu-9.2
# cmake version 3.30.4
cmake --debug-find \
-DMPI_C_COMPILER=$(which mpicc) \
-DMPI_CXX_COMPILER=$(which mpicxx) \
-DMPI_HOME=$(which mpirun) \
-Dwith-mpi=ON \
-Dwith-openmp=ON \
-DCYTHON_EXECUTABLE=/<some_path>/intel/oneapi/2022.1/intelpython/latest/bin/cython \
-DCMAKE_INSTALL_PREFIX:PATH=/<some_path>/nest-simulator-3.8-build \
/<path_to_extracted_tar>/nest-simulator-3.8/
# if I don't specify the Cython path, cmake picks an outdated (uncompatible) cython version. I did not try the -Dcythonize-pynest=OFF option because I don't know how to build PyNEST from a pre-cythonized pynestkernel.pyx.
make
make install
make installcheck
```
Once this finishes, I do the usual `source`-ing of `nest_vars.sh`. I also add the NEST path to my python venv's `site-packages`. This has always worked for all NEST versions I ever installed.
`installcheck` finishes with 1 error. See below:
```
THE NEST TESTSUITE DISCOVERED PROBLEMS
The following tests failed
| regressiontests.issue-1703.py
Please report test failures by creating an issue at
https://github.com/nest/nest-simulator/issues
---------------------------------------------------------------------------
make[3]: *** [CMakeFiles/installcheck] Error 1
make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2
make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2
make: *** [installcheck] Error 2
```
THE WARNING:
Ignoring this, if I proceed with pyNEST in the venv by `import nest`, I get the following warning:
```
--------------------------------------------------------------------------
WARNING: There is at least non-excluded one OpenFabrics device found,
but there are no active ports detected (or Open MPI was unable to use
them). This is most certainly not what you wanted. Check your
cables, subnet manager configuration, etc. The openib BTL will be
ignored for this job.
Local host: n4669
--------------------------------------------------------------------------
n4669.nemo.privat.74030PSM2 no hfi units are active (err=23)
--------------------------------------------------------------------------
Open MPI failed an OFI Libfabric library call (fi_endpoint). This is highly
unusual; your job may behave unpredictably (and/or abort) after this.
Local host: n4669
Location: mtl_ofi_component.c:627
Error: Invalid argument (22)
--------------------------------------------------------------------------
-- N E S T --
Copyright (C) 2004 The NEST Initiative
Version: 3.8.0
Built: Oct 10 2024 16:21:41
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.
```
THE CRASH:
If I ignore this warning and proceed to submit a job, the execution eventually crashes with exit code: 134. If you'd like to see the crash dump, check this MD file on GitLab.: https://gitlab.rz.uni-freiburg.de/as2013/mpi-hpc-nestv3.8.git
Any idea what's going wrong here?
If I follow the same build and installation steps on my local machine (other than specifying the Cython path in cmake; because no need). Neither do I get any warnings nor does any simulation crash.
I'm guessing this has to do with the build and installation on the cluster.
I'd appreciate any input. Thanks!
Best,
Ady
Hello everyone,
Is there a NESTML version of the NEST model aeif_cond_beta_multisynapse ? (https://nest-simulator.readthedocs.io/en/stable/models/aeif_cond_beta_multi…)
If not, is there any difficulties that I might face implementing it in NESTML that I need to be aware of ? (Like how to handle multiple types of synapses).
Best,
Tanguy
Dear NEST Users & Developers!
I would like to invite you to our next fortnightly Open NEST Developer Video Conference today
*Monday October 7, at 11:30 CEST (UTC+0200).*
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/2024-10-07-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-10-07-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
----------------------------------------------------------------------
