Dear Colleagues,
The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NEST Simulator to the NEST Conference 2022. The 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 explicitly encourage young scientists to participate in the conference!
This year's conference will again take place as a virtual conference on Thursday/Friday 23/24 June 2022.
Submission of contributions is now open!
We are inviting contributions to the conference, including talks, "posters" and workshops on specific topics.
Please register and submit your contribution(s) via the conference website
https://nest-simulator.org/conference.
Important dates
30 April 2022 - Deadline for NEST Initiative membership applications eligible for fee reduction
11 May 2022 - Deadline for submission of contributions
03 June 2022 - Notification of acceptance
17 June 2022 - Registration deadline
23 June 2022 - NEST Conference 2022 starts
We are looking forward to seeing you all in June!
Hans Ekkehard Plesser and the conference organizing committee
--
Prof. Dr. Hans Ekkehard Plesser
Head, 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!
I've found an implementation of
"Synchrony generation in recurrent networks with frequency-dependent
synapses" Tsodyks, Uziel, Markram 2000
in
https://github.com/uahic/Nest_2_10_release/blob/d3a7b0b8105622b40ef87d8a5ba…
but it's missing in the latest versions of NEST.
Is there a comparable implementation in a recent NEST release?
Preferably in Python?
Thanks in advance,
Sebastian
Dear colleagues,
We are looking for a new NEST developer to join the NEST team at NMBU in Ås, Norway, as head engineer or senior engineer. The position is funded by the Human Brain Project, available immediately and limited to 30 September 2023. Application deadline is 26 April 2023.
For details, please see https://www.jobbnorge.no/en/available-jobs/job/224028/head-engineer-senior-… or get in touch with me.
Best regards,
Hans Ekkehard
--
Prof. Dr. Hans Ekkehard Plesser
Head, 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 March 14, 11.30-12.30 CEST (UTC+2).
/Note/ that we changed to daylight savings time (aka "summer time") and are now UTC+2.
Feel free to join the meeting also just to bring your own questions for
direct discussion in the in-depth section.
As usual, in the Project team round, a contact person of each team will
give a short statement summarizing ongoing work in the team and
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.
Agenda
* Welcome
* Review of NEST User Mailing List
* Project team round
* In-depth discussion
* Inclusion of NEST-GPU by Golosio et al.
The agenda for this meeting is also available online, see
https://github.com/nest/nest-simulator/wiki/2022-03-28-Open-NEST-Developer-…
Looking forward to seeing you soon!
Cheers,
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 Team,
working with Python 3.8 and Nest 3.2 my goal is, after creating a spatial NodeCollection "neurons", to create a new NodeCollection containing a selection of the node from "neurons".
To achieve this I tried two different approaches:
1. Create a Mask object and use nest.SelectNodesByMask()
nodes_in_mask = nest.SelectNodesByMask(neurons, ctr_position, mask_obj)
2. Transform the NodeCollection into a list of node ids, pick 3 random ids, and create a new NodeCollection containing those 3 Nodes
neurons_list = neurons.tolist()
for x in range(0, 3):
center = random.choice(neurons_list)
node_ids.append(center)
node_ids.sort()
new_collection = nest.NodeCollection(node_ids)
But with both approaches I get the same problems that some Information (of the positions) seems to go missing. This shows in different ways.
First the new NodeCollections are no longer spatial (nodes_in_mask.spatial and new_collection.spatial return none).
Second trying to get the node Positions results in an Error:
nest.GetPosition(nodes_in_mask)
-> Error #1 nest.lib.hl_api_exceptions.LayerExpected: LayerExpected in SLI function GetPosition_g:
And last, trying to Plot the Layer also results in an Error:
fig = nest.PlotLayer(nodes_in_mask)
-> Error #2 TypeError: 'NoneType' object is not subscriptable
I attached a .txt file containing py code showing the problems.
Why do those Problems occur and what can I do to solve them?
Is there a way to create an empty NodeCollection s.t. I can add the wished nodes one by one?
What exactly does the metadata of a Nodecollection represent? Is there a way to set it manually for example to spatial?
Thank you in advance for your Answers,
Miriam
Hi,
Any neuron model built with NESTML and installed via nest.Install('mymodule') receives 'UnknownNode' as the value for 'model':
> nrn.get('model')
> 'UnknownNode'
Can this be ignored by users? Is it possible to set the value in .nestml file for compatibility with standard models?
Best regards,
Alex.
Dear NEST Users & Developers!
I would like to invite you to our next fortnightly Open NEST Developer
Video Conference, today
Monday March 14, 11.30-12.30 CET (UTC+1).
Feel free to join the meeting also just to bring your own questions for
direct discussion in the in-depth section.
As usual, in the Project team round, a contact person of each team will
give a short statement summarizing ongoing work in the team and
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.
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/2022-03-14-Open-NEST-Developer-…
Looking forward to seeing you soon!
Cheers,
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 all,
Apologies for the cross-posts.
We, the INCF/OCNS Software working group, are conducting a short
anonymous survey to collect information on the usage of common software
tools in comp-neuro. Could we please request you to spend 2 minutes of
your time to fill it out here:
https://forms.gle/NXWv2CwtWBSB9BXv9
The information gathered in the survey will be used to organise
sessions/workshops related to the software, and improve awareness about
them and their maintenance.
On behalf of the Software WG,
--
Thanks,
Regards,
Ankur Sinha (He / Him / His)
Research Fellow at the Silver Lab | http://silverlab.org/
Department of Neuroscience, Physiology, & Pharmacology
University College London, London, UK
Time zone: Europe/London
Dear NESTML Users,
when I try the NESTML Izhikevich tutorial, I have a problem in the generate_nest_target function. The output in the terminal is the following:
***
-- N E S T --
Copyright (C) 2004 The NEST Initiative
Version: UNKNOWN
Built: Jan 18 2022 13:53:41
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 CXX compiler identification is GNU 9.3.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-------------------------------------------------------
nestml_izhikevich_module Configuration Summary
-------------------------------------------------------
C++ compiler : /usr/bin/c++
Build static libs : OFF
C++ compiler flags :
NEST compiler flags : -std=c++11 -O2 -Wall -fopenmp -pthread -fdiagnostics-color=auto
NEST include dirs : -I/opt/nest/include/nest -I/usr/include -I/usr/include -I/usr/include -I/opt/music-install/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/include
NEST libraries flags : -L/opt/nest/lib/nest -lnestutil -lnest -lsli -lnestkernel -fopenmp /usr/lib/x86_64-linux-gnu/libltdl.so /usr/lib/x86_64-linux-gnu/libreadline.so /usr/lib/x86_64-linux-gnu/libncurses.so /usr/lib/x86_64-linux-gnu/libgsl.so /usr/lib/x86_64-linux-gnu/libgslcblas.so /opt/music-install/lib/libmusic.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
-------------------------------------------------------
You can now build and install 'nestml_izhikevich_module' using
make
make install
The library file libnestml_izhikevich_module.so will be installed to
/opt/nest/lib/nest
The module can be loaded into NEST using
(nestml_izhikevich_module) Install (in SLI)
nest.Install(nestml_izhikevich_module) (in PyNEST)
CMake Warning (dev) in CMakeLists.txt:
No cmake_minimum_required command is present. A line of code such as
cmake_minimum_required(VERSION 3.22)
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 done
-- Generating done
-- Build files have been written to: /tmp/nestml-component
[ 16%] Building CXX object CMakeFiles/nestml_izhikevich_module_module.dir/nestml_izhikevich_module.o
In file included from /opt/nest/include/nest/connector_base.h:35,
from /opt/nest/include/nest/connection_manager.h:36,
from /opt/nest/include/nest/connection_manager_impl.h:26,
from /tmp/nestml-component/nestml_izhikevich_module.cpp:26:
/opt/nest/include/nest/sort.h:36:10: fatal error: boost/sort/spreadsort/spreadsort.hpp: No such file or directory
36 | #include <boost/sort/spreadsort/spreadsort.hpp>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/nestml_izhikevich_module_module.dir/build.make:76: CMakeFiles/nestml_izhikevich_module_module.dir/nestml_izhikevich_module.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:112: CMakeFiles/nestml_izhikevich_module_module.dir/all] Error 2
make: *** [Makefile:156: all] Error 2
***
While the Jupyter notebook output is the following:
***
Warning: PyGSL is not available. The stiffness test will be skipped.
Warning: No module named 'pygsl'
Option "nest_path" does not exist in builder
---------------------------------------------------------------------------
CalledProcessError Traceback (most recent call last)
/opt/data/nestml/pynestml/codegeneration/nest_builder.py in build(self)
149 try:
--> 150 subprocess.check_call(make_all_cmd, stderr=subprocess.STDOUT, shell=shell,
151 cwd=str(os.path.join(target_path)))
/usr/lib/python3.8/subprocess.py in check_call(*popenargs, **kwargs)
363 cmd = popenargs[0]
--> 364 raise CalledProcessError(retcode, cmd)
365 return 0
CalledProcessError: Command '['make', 'all']' returned non-zero exit status 2.
During handling of the above exception, another exception occurred:
GeneratedCodeBuildException Traceback (most recent call last)
<ipython-input-2-f7696df63255> in <module>
----> 1 generate_nest_target(input_path="izhikevich_solution.nestml",
2 target_path="/tmp/nestml-component",
3 module_name="nestml_izhikevich_module",
4 suffix="_nestml",
5 logging_level="ERROR",
/opt/data/nestml/pynestml/frontend/pynestml_frontend.py in generate_nest_target(input_path, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts)
181 A dictionary containing additional options for the target code generator.
182 """
--> 183 generate_target(input_path, target_platform="NEST", target_path=target_path, logging_level=logging_level,
184 module_name=module_name, store_log=store_log, suffix=suffix, install_path=install_path,
185 dev=dev, codegen_opts=codegen_opts)
/opt/data/nestml/pynestml/frontend/pynestml_frontend.py in generate_target(input_path, target_platform, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts)
150 FrontendConfiguration.set_codegen_opts(codegen_opts)
151
--> 152 if not process() == 0:
153 raise Exception("Error(s) occurred while processing the model")
154
/opt/data/nestml/pynestml/frontend/pynestml_frontend.py in process()
278 options=FrontendConfiguration.get_codegen_opts())
279 if _builder is not None:
--> 280 _builder.build()
281
282 if FrontendConfiguration.store_log:
/opt/data/nestml/pynestml/codegeneration/nest_builder.py in build(self)
151 cwd=str(os.path.join(target_path)))
152 except subprocess.CalledProcessError as e:
--> 153 raise GeneratedCodeBuildException('Error occurred during \'make all\'! More detailed error messages can be found in stdout.')
154
155 # finally execute make install
GeneratedCodeBuildException: Error occurred during 'make all'! More detailed error messages can be found in stdout.
***
I installed Boost with 'sudo apt-get install libboost-all-dev' from the terminal.
Can you help me?
Best,
Salvo
Dear NESTML Users,
In the last post I fixed a problem that was related to the fact that in the 'izhikevich_solution.nestml' the first line was commented.
Now, after following the guide in "https://nestml.readthedocs.io/en/latest/installation.html" related to the NESTML
installation, I tried to follow the NESTML Izhikevich tutorial in "https://nestml.readthedocs.io/en/latest/tutorials/izhikevich/nestml_izhikev…". After installing the cmake with "pip install cmake", when I execute the following part of the tutorial:
generate_nest_target(input_path="izhikevich_solution.nestml",
target_path="/tmp/nestml-component",
logging_level="ERROR",
codegen_opts={"nest_path":
NEST_SIMULATOR_INSTALL_LOCATION})
I obtain the following error:
Warning: PyGSL is not available. The stiffness test will be skipped.
Warning: No module named 'pygsl'
Option "nest_path" does not exist in builder
---------------------------------------------------------------------------
CalledProcessError Traceback (most recent call last)
/opt/data/nestml/pynestml/codegeneration/nest_builder.py in build(self)
149 try:
--> 150 subprocess.check_call(make_all_cmd, stderr=subprocess.STDOUT, shell=shell,
151 cwd=str(os.path.join(target_path)))
/usr/lib/python3.8/subprocess.py in check_call(*popenargs, **kwargs)
363 cmd = popenargs[0]
--> 364 raise CalledProcessError(retcode, cmd)
365 return 0
CalledProcessError: Command '['make', 'all']' returned non-zero exit status 2.
During handling of the above exception, another exception occurred:
GeneratedCodeBuildException Traceback (most recent call last)
<ipython-input-2-f0909be085f4> in <module>
----> 1 generate_nest_target(input_path="izhikevich_solution.nestml",
2 target_path="/tmp/nestml-component",
3 module_name="nestml_izhikevich_module",
4 suffix="_nestml",
5 logging_level="ERROR",
/opt/data/nestml/pynestml/frontend/pynestml_frontend.py in generate_nest_target(input_path, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts)
181 A dictionary containing additional options for the target code generator.
182 """
--> 183 generate_target(input_path, target_platform="NEST", target_path=target_path, logging_level=logging_level,
184 module_name=module_name, store_log=store_log, suffix=suffix, install_path=install_path,
185 dev=dev, codegen_opts=codegen_opts)
/opt/data/nestml/pynestml/frontend/pynestml_frontend.py in generate_target(input_path, target_platform, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts)
150 FrontendConfiguration.set_codegen_opts(codegen_opts)
151
--> 152 if not process() == 0:
153 raise Exception("Error(s) occurred while processing the model")
154
/opt/data/nestml/pynestml/frontend/pynestml_frontend.py in process()
278 options=FrontendConfiguration.get_codegen_opts())
279 if _builder is not None:
--> 280 _builder.build()
281
282 if FrontendConfiguration.store_log:
/opt/data/nestml/pynestml/codegeneration/nest_builder.py in build(self)
151 cwd=str(os.path.join(target_path)))
152 except subprocess.CalledProcessError as e:
--> 153 raise GeneratedCodeBuildException('Error occurred during \'make all\'! More detailed error messages can be found in stdout.')
154
155 # finally execute make install
GeneratedCodeBuildException: Error occurred during 'make all'! More detailed error messages can be found in stdout.
So, the "nest_path" keyword does not exist. Can anyone help me?
Best,
Salvo