Dear Jasper,
In NEST 3, this should be possible.
Stine or Håkon, could you provide some advice?
Best,
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
On 06/04/2021, 12:05, "Albers, Jasper" <j.albers(a)fz-juelich.de<mailto:j.albers@fz-juelich.de>> wrote:
Dear all,
a colleague of mine (in CC) and myself are implementing a spatially structured network in NEST (using current NEST master). We are wondering how to generate a population of neurons that are distributed on a regular grid plus a random jitter. This means that we want to end up with a spatial distribution as can be seen in Figure 8 in the tutorial for creating spatially structured networks<https://nest-simulator.readthedocs.io/en/latest/tutorials/pynest_tutorial/p…>. Below that figure one finds a code snippet; however, we believe that this does not correspond to the distribution of Figure 8.
In the documentation of NEST 2.20.1 we did find a code snippet that produces a jittered grid:
import numpy as np
# grid with jitter
jit = 0.03
xs = np.arange(-0.5,.501,0.1)
poss = [[x,y] for y in xs for x in xs]
poss = [[p[0]+np.random.uniform(-jit,jit),p[1]+np.random.uniform(-jit,jit)] for p in poss]
layer_dict_ex = {"positions": poss,
"extent" : [1.1,1.1],
"elements" : "iaf_psc_alpha"}
As is apparent, this code does not make use of NEST internal random number generation but rather produces a list of positions that is then passed to a layer.
Thus our question is: is it possible to create a jittered grid natively in NEST master?
Best regards,
Jasper and Anno
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Frauke Melchior
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Dear all,
a colleague of mine (in CC) and myself are implementing a spatially structured network in NEST (using current NEST master). We are wondering how to generate a population of neurons that are distributed on a regular grid plus a random jitter. This means that we want to end up with a spatial distribution as can be seen in Figure 8 in the tutorial for creating spatially structured networks<https://nest-simulator.readthedocs.io/en/latest/tutorials/pynest_tutorial/p…>. Below that figure one finds a code snippet; however, we believe that this does not correspond to the distribution of Figure 8.
In the documentation of NEST 2.20.1 we did find a code snippet that produces a jittered grid:
import numpy as np
# grid with jitter
jit = 0.03
xs = np.arange(-0.5,.501,0.1)
poss = [[x,y] for y in xs for x in xs]
poss = [[p[0]+np.random.uniform(-jit,jit),p[1]+np.random.uniform(-jit,jit)] for p in poss]
layer_dict_ex = {"positions": poss,
"extent" : [1.1,1.1],
"elements" : "iaf_psc_alpha"}
As is apparent, this code does not make use of NEST internal random number generation but rather produces a list of positions that is then passed to a layer.
Thus our question is: is it possible to create a jittered grid natively in NEST master?
Best regards,
Jasper and Anno
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Frauke Melchior
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Dear NEST Users & Developers!
I would like to invite you to our next fortnightly Open NEST Developer
Video Conference, today
Monday 29 March, 11.30-12.30 CEST (UTC+2).
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.
Today we have two potential topics for the in-depth discussion. The
first is probably not that much to discuss, but we'd be interested in
everyone's point of view. The second one touches many areas of the
simulator and new scientific use-cases.
Agenda
Welcome
Review of NEST User Mailing List
Project team round
In-depth discussion
* CMake targets vs. CMake flags #1905 Microhackathon
* Discuss dump/reload of connectivity (/not/ checkpointing!)
The agenda for this meeting is also available online, see
https://github.com/nest/nest-simulator/wiki/2021-03-29-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 all,
is it possible to assign the weight recorder to a synapse /after /the
network is created? In the Neurorobotics Platform we allow the user to
add devices (this can be additional nodes, or current inputs via
SetStatus) after the creation of the network and it would be nice to
also add recorders/readouts for spikes and weights. For spike recorders
and multimeters this is possible as just a new node with a new
connection is added.
Thanks!
Best Regards,
Benedikt
--
Benedikt Feldotto M.Sc.
Research Assistant
Human Brain Project - Neurorobotics
Technical University of Munich
Department of Informatics
Chair of Robotics, Artificial Intelligence and Real-Time Systems
Room HB 2.02.20
Parkring 13
D-85748 Garching b. München
Tel.: +49 89 289 17628
Mail: feldotto(a)in.tum.de
https://www6.in.tum.de/en/people/benedikt-feldotto-msc/www.neurorobotics.net
Dear NEST Users & Developers!
I would like to invite you to our next fortnightly Open NEST Developer
Video Conference, today
Monday 15 March, 11.30-12.30 CET (UTC+1).
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.
Today this would for example be a discussion about the mechanisms of the
Python module installation.
Agenda
Welcome
Review of NEST User Mailing List
Project team round
In-depth discussion
* Python installation of NEST, see
[#1948](https://github.com/nest/nest-simulator/issues/1948),
[#1959](https://github.com/nest/nest-simulator/pull/1959)
The agenda for this meeting is also available online, see
https://github.com/nest/nest-simulator/wiki/2021-03-15-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 all,
maybe I am overlooking something, I am searching for a spike frequency
generator without noise. I was looking at the poisson generator, but as
far as I can see there is no parameter to adjust/remove the noise. Is
there any node available that takes as input a frequency and outputs
spikes at this given frequency?
Thanks!
Best,
Benedikt
--
Benedikt Feldotto M.Sc.
Research Assistant
Human Brain Project - Neurorobotics
Technical University of Munich
Department of Informatics
Chair of Robotics, Artificial Intelligence and Real-Time Systems
Room HB 2.02.20
Parkring 13
D-85748 Garching b. München
Tel.: +49 89 289 17628
Mail: feldotto(a)in.tum.de
https://www6.in.tum.de/en/people/benedikt-feldotto-msc/www.neurorobotics.net
Dear Nest Community,
Has anyone encountered a "bad_alloc" error like the one below and if so,
any recommendations? It appears to be a VM memory issue but only using
21% of harddrive space (ref: below).
My simulation successfully completes for 200,000 ms but errors out at 98%
complete for 230,000 ms, 75% for 300,000 ms and 56% for 400,000 ms.
I'm running on NEST 2.18.0 VirtualBox lubuntu 18.04 (ref: image of
settings below).
Thank you for any suggestions.
Best Regards,
--Allen
**********************************************
**** Error Message *****
>> # SIMULATION
>> nest.Simulate(300000)
Nov 21 17:10:28 NodeManager::prepare_nodes [Info]:
Preparing 684 nodes for simulation.
Nov 21 17:10:28 MUSICManager::enter_runtime [Info]:
Entering MUSIC runtime with tick = 1 ms
Nov 21 17:10:28 SimulationManager::start_updating_ [Info]:
Number of local nodes: 684
Simulation time (ms): 300000
Number of OpenMP threads: 2
Number of MPI processes: 1
75 %: network time: 223698.0 ms, realtime factor: 0.6277Traceback (most
recent call last):
File "<stdin>", line 3, in <module>
File
"/home/nest/work/nest-install/lib/python3.6/site-packages/nest/ll_api.py",
line 246, in stack_checker_func
return f(*args, **kwargs)
File
"/home/nest/work/nest-install/lib/python3.6/site-packages/nest/lib/hl_api_simulation.py",
line 66, in Simulate
sr('ms Simulate')
File
"/home/nest/work/nest-install/lib/python3.6/site-packages/nest/ll_api.py",
line 132, in catching_sli_run
raise exceptionCls(commandname, message)
nest.ll_api.std::bad_alloc: ('std::bad_alloc in Simulate_d: C++ exception:
std::bad_alloc', 'std::bad_alloc', <SLILiteral: Simulate_d>, ': C++
exception: std::bad_alloc')
********************************************
**** Folder Space on VirtualBox after Error ****
nest@nestvm:~$ df -h
Filesystem Size Used Avail Use% Mounted on
udev 5.2G 0 5.2G 0% /dev
tmpfs 1.1G 1.1M 1.1G 1% /run
/dev/sda1 99G 20G 76G 21% /
tmpfs 5.2G 0 5.2G 0% /dev/shm
tmpfs 5.0M 4.0K 5.0M 1% /run/lock
tmpfs 5.2G 0 5.2G 0% /sys/fs/cgroup
SharedNest2 917G 447G 470G 49% /media/sf_SharedNest2
tmpfs 1.1G 16K 1.1G 1% /run/user/1000
/dev/sr0 74M 74M 0 100% /media/nest/VBox_GAs_6.0.10
***********************************
**** VirtualBox Settings *******
[image: image.png]
Dear NEST Developers,
With #1972, which I just merged into the master branch, the C++ file names for the synapse models have changed from
xyz_connection.h
to
xyz_synapse.h
to make them consistent with the model names we have on the user side.
Please pull this change into your branches as soon as possible. This is purely a behind-the-scenes change which does not affect users.
Best,
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