Dear NEST developer,
I would like to initialize a network with neurons and connections and then
run many simulations with it. It would be great if I could build the
network one time and then deepcopy (or something similar) for each
simulation. Is something like this possible?
Thanks,
Andrew Lehr
Dear NEST Users & Developers!
I would like to invite you to our next bi-weekly Open NEST Developer
Video Conference, today
Monday 30 March, 11.30-12.30 CEST (UTC+2).
Given the current circumstances today's meeting will be again via video
conference only, so please do not meet in person! Stay safe!
We discuss development status of relevant pull-requests/issues for the
upcoming releases.
Agenda
Welcome
Review of NEST User Mailing List
Projects & Branches
Review of open Github Pull Request
Review of open Github Issues
The agenda for this meeting is also available online, see
https://github.com/nest/nest-simulator/wiki/2020-03-30-Open-NEST-Developer-…
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 all,
Hope everyone is staying safe and well in these difficult times.
I am an undergrad who is just getting started with this library, so I want to apologize in advance for the basic question. I am having issues I believe are memory-related when I call GetConnections on rather small networks. Here is my script:
import nest
# memory testing
nest.ResetKernel()
n = 5 # number of neurons
epop1 = nest.Create("iaf_psc_alpha",n)
epop2 = nest.Create("iaf_psc_alpha",n)
nest.Connect(epop1,epop2,{'rule': 'all_to_all'})
# we can now query the synapses using GetConnections
conns = nest.GetConnections(epop1,target = epop2)
nest.GetStatus(conns,["target","weight"])
This runs fine for n < 5, but I get the following error with n >=5:
Assertion failed: (source_lid < MAX_LID), function set_source_lid, file /usr/local/miniconda/conda-bld/nest-simulator_1583214474797/work/nestkernel/target_data.h, line 264.
Abort trap: 6
I have run some of the example scripts like brunel_alpha_numpy with a few thousand neurons and they work just fine.
Am I making an improper call to GetConnections here? And if so, what is a better way to dynamically check connectivity?
Alternatively, might there be something wrong with my Nest environment? And if so, what should I look at to troubleshoot this?
Thank you so much for your help.
Best wishes,
Josh
Hello everyone!
I tried installing nest using cmake version 3.14 on ubuntu.
This is the command I tried from the nest-simulator directory:
cmake -DCMAKE_INSTALL_PREFIX:PATH=/home/bsvogler/Dokumente/nest /home/bsvogler/Dokumente/nest-simulator/nest
I get the following two error messages and cannot find any information on how to resolve this issue
=========
CMake Error at CMakeLists.txt:97 (install):
install TARGETS given no RUNTIME DESTINATION for executable target "nest".
CMake Error at CMakeLists.txt:106 (FILTER_HEADERS):
Unknown CMake command "FILTER_HEADERS".
CMake Warning (dev) in CMakeLists.txt:
No cmake_minimum_required command is present. A line of code such as
cmake_minimum_required(VERSION 3.13)
should be added at the top of the file. The version specified may be lower
if you wish to support older CMake versions for this project. For more
information run "cmake --help-policy CMP0000".
This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring incomplete, errors occurred!
See also "/home/bsvogler/Dokumente/nest-simulator/nestinstall/CMakeFiles/CMakeOutput.log".
=======
I tried the master branch and the nest3 branch. I need a working nest 3 simulator.
I managed to compile just yesterday but in the meantime, I reinstalled the operating system.
Please help me out.
Kind regards,
Benedikt S. Vogler
Dear all,
I would like to receive a continuous stream of data via ‘music_cont_in_proxy’ and use it as input current to a neuron. I used ‘iaf_cond_alpha_mc’ as model neuron because I could specify the input that should target the neuron via the receptor_type that accepts current {‘receptor_type’: 7} (’soma_curr’: 7) and connected the ‘music_cont_in_proxy’ via this receptor to the neuron. Currently, for testing purposes, I used ‘constsource’ music binary continuous data stream, which is also used in NEST guides (https://bit.ly/2xBNfpO). As I imagined, it didn’t work maybe because the output type of the music port doesn’t match the input type of the receptor type (’the following error’). Does anyone know how I can overcome this problem (that I can use ‘music_cont_in_proxy’ as current source)? Thank you very much in advance.
########ERROR########
Traceback (most recent call last):
File "./conttest.py", line 39, in <module>
nest.Connect(mcip, mc, 'one_to_one', {'receptor_type': 7})
File "/local/work/Projects/closed-loop-learning/NEST/lib/python3.7/site-packages/nest/ll_api.py", line 246, in stack_checker_func
return f(*args, **kwargs)
File "/local/work/Projects/closed-loop-learning/NEST/lib/python3.7/site-packages/nest/lib/hl_api_connections.py", line 362, in Connect
sr('Connect')
File "/local/work/Projects/closed-loop-learning/NEST/lib/python3.7/site-packages/nest/ll_api.py", line 132, in catching_sli_run
raise exceptionCls(commandname, message)
nest.ll_api.UnexpectedEvent: ('UnexpectedEvent in Connect_g_g_D_D: Node cannot handle received event.', 'UnexpectedEvent', <SLILiteral: Connect_g_g_D_D>, ': Node cannot handle received event.’)
########ERROR########
Best wishes,
Mohammad
--
Mohammadreza Mohagheghi Nejad
Postdoctoral researcher in computational neuroscience,
Institute of Neural Computation,
Ruhr University Bochum, Germany
https://www.ini.rub.de/the_institute/people/mohammadreza-mohagheghi_nejad/
Dear all,
I am trying to use music ports for my simulations, which requires
continuous transmission of data to NEST. I would like to test them in a toy
example before integrating them in my project to make sure I am using them
as I should. So, under section "Receiving continuous data" in "Guides\Using
NEST with MUSIC" (
https://nest-simulator.readthedocs.io/en/stable/guides/using_nest_with_musi…),
I found a guide for this functionality of NEST, however, the binary
"constsource" is not available. Does anybody have any idea where I can find
it?
Thank you very much in advance for your help,
Best wishes,
Mohammad
--
Mohammadreza Mohagheghi Nejad
Postdoctoral researcher in computational neuroscience,
Institute of Neural Computation,
Ruhr University Bochum, Germany
https://www.ini.rub.de/the_institute/people/mohammadreza-mohagheghi_nejad/
Dear NEST Users & Developers!
I would like to invite you to our next bi-weekly Open NEST Developer
Video Conference, today
Monday 16 March, 11.30-12.30 CET (UTC+1).
Given the current circumstances today's meeting will be *via VIDEO
CONFERENCE**ONLY*, so please do not meet in person!
We will focus on the organization of our now even more decentralized
work and discuss development status of relevant pull-requests/issues for
the upcoming releases.
Agenda
Welcome
Review of NEST User Mailing List
Review of open Github Pull Request
Review of open Github Issues
The agenda for this meeting is also available online, see
https://github.com/nest/nest-simulator/wiki/2020-03-16-Open-NEST-Developer-…
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
Dear NEST Developers!
If you currently have an open pull request against the NEST master branch on Github, please merge the most recent updates from master into your branch. A bug described in #1449 and fixed by #1458 lead to non-deterministic test suite failures.
Once you have merged master into your branch, please push again to Github to re-run the tests on Travis.
Best,
Hans Ekkehard
--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
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
Home http://arken.nmbu.no/~plesser
Dear community,
Sorry if this is off-topic for this list, but I am facing a problem with NESTML.
After compiling any of the example neuron models present in the
repository, the model seems not to have parameters inherited from
ArchivingNode (such as, for instance, an STDP parameter tau_minus)
available for GetStatus() or SetStatus(). Oddly enough, the model
probably does possess these parameters, because can be connected
to/from TDP synapses, but just does not expose them to Get/SetStatus.
Could you please advise what I should do to examine the problem?
I am using NEST version 2.20 and NESTML version 3.0.post0.dev5 (pip-installed).
Faithfully yours,
Alex Serenko,
graduate student at Kurchatov Institute, Moscow, Russia
Hello everyone!
I am transitioning my Code from nest 2 to nest 3.
In nest 2 I used a list of connections and could use this list with nest.Get/SetStatus().
With nest 3 I now have a list of SynapseCollections instances, where each synapse collection contains only one connection. For node collections, there seems to be an operator to create a composite (https://nest-simulator.readthedocs.io/en/latest/guides/from_nest2_to_nest3.…). For SynapseCollections, however, I was unable to use the plus operator and could not find similar documentation as in the transition guide. My current workaround is to loop over each instance the list and call Set() on each instance/synapse. What is the recommended way to create a SynapseCollections from many?
Is there somewhere more documentation covering nest 3 than the two pages covering the changes form nest 2 to 3?
Kind regards,
Benedikt S. Vogler