12 Apr
2023
12 Apr
'23
10:25 p.m.
Dear all,
While I try to solve my doubts on the other thread, I decided to try nestml on my own.
For this, I installed docker and did:
wget
https://raw.githubusercontent.com/steffengraber/nest-docker/master/docker-c…
and then:
docker-compose up nest-jupyterlab
as explained here:
https://nest-simulator.readthedocs.io/en/latest/installation/docker.html#do…
Then, I created a silly Python file that simply does:
import matplotlib.pyplot as plt
import nest
import numpy as np
import os
from pynestml.frontend.pynestml_frontend import generate_nest_target
NEST_SIMULATOR_INSTALL_LOCATION = nest.ll_api.sli_func("statusdict/prefix ::")
generate_nest_target(input_path="izhikevich.nestml",
target_path="/tmp/nestml-component",
logging_level="ERROR",
codegen_opts={"nest_path":
NEST_SIMULATOR_INSTALL_LOCATION})
where izhikevich.nestml is nothing else than a brute-force copy and paste of
https://github.com/nest/nestml/blob/master/models/neurons/izhikevich.nestml
It should be trivial, but then I get:
-- N E S T --
Copyright (C) 2004 The NEST Initiative
Version: 3.4
Built: Mar 31 2023 12:33:35
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.
WARNING:root:PyGSL is not available. The stiffness test will be skipped.
WARNING:root:Error when importing: No module named 'pygsl'
line 44:4 extraneous input 'equations' expecting {NEWLINE, 'end',
'inline', 'recordable', NAME}
line 48:4 extraneous input 'parameters' expecting {NEWLINE, 'end',
'inline', 'recordable', 'kernel', NAME}
line 59:4 missing 'end' at 'input'
line 63:4 extraneous input 'output' expecting {NEWLINE, 'end', NAME}
line 77:24 mismatched input '<EOF>' expecting {'end',
'elif', 'else'}
[6,GLOBAL, ERROR]: Error occurred during parsing: abort
Traceback (most recent call last):
File "/opt/data/Izhikevich.py", line 10, in <module>
generate_nest_target(input_path="izhikevich.nestml",
File
"/usr/local/lib/python3.10/dist-packages/pynestml/frontend/pynestml_frontend.py",
line 229, in generate_nest_target
generate_target(input_path, target_platform="NEST", target_path=target_path,
logging_level=logging_level,
File
"/usr/local/lib/python3.10/dist-packages/pynestml/frontend/pynestml_frontend.py",
line 199, in generate_target
raise Exception("Error(s) occurred while processing the model")
Exception: Error(s) occurred while processing the model
which I do not understand. The syntaxis of nestml seems clear, no "end",
right? Then, what am I doing wrong?
Thanks!
gus.-
PS: I still have my doubts, as explained in the other thread, but I thought this is a
different issue... sorry if I did wrong!!!
13 Apr
13 Apr
9:47 a.m.
Hello Gustavo,
The “end” keyword was removed recently in NESTML and is not part of a release version yet.
I suppose the docker container will have the last released version of NESTML (v5.2.0)
which still has the “end” keyword in the models.
The Izhikevich neuron model with “end” keyword can be found here:
https://github.com/nest/nestml/blob/v5.2.0/models/neurons/izhikevich.nestml
Please try this model and let us know if you face any issues.
Thanks,
Pooja
On 12. Apr 2023, at 22:25, gustavo.patow(a)udg.edu
wrote:
Dear all,
While I try to solve my doubts on the other thread, I decided to try nestml on my own.
For this, I installed docker and did:
wget
https://raw.githubusercontent.com/steffengraber/nest-docker/master/docker-c…
and then:
docker-compose up nest-jupyterlab
as explained here:
https://nest-simulator.readthedocs.io/en/latest/installation/docker.html#do…
Then, I created a silly Python file that simply does:
import matplotlib.pyplot as plt
import nest
import numpy as np
import os
from pynestml.frontend.pynestml_frontend import generate_nest_target
NEST_SIMULATOR_INSTALL_LOCATION = nest.ll_api.sli_func("statusdict/prefix ::")
generate_nest_target(input_path="izhikevich.nestml",
target_path="/tmp/nestml-component",
logging_level="ERROR",
codegen_opts={"nest_path":
NEST_SIMULATOR_INSTALL_LOCATION})
where izhikevich.nestml is nothing else than a brute-force copy and paste of
https://github.com/nest/nestml/blob/master/models/neurons/izhikevich.nestml
It should be trivial, but then I get:
-- N E S T --
Copyright (C) 2004 The NEST Initiative
Version: 3.4
Built: Mar 31 2023 12:33:35
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.
WARNING:root:PyGSL is not available. The stiffness test will be skipped.
WARNING:root:Error when importing: No module named 'pygsl'
line 44:4 extraneous input 'equations' expecting {NEWLINE, 'end',
'inline', 'recordable', NAME}
line 48:4 extraneous input 'parameters' expecting {NEWLINE, 'end',
'inline', 'recordable', 'kernel', NAME}
line 59:4 missing 'end' at 'input'
line 63:4 extraneous input 'output' expecting {NEWLINE, 'end', NAME}
line 77:24 mismatched input '<EOF>' expecting {'end',
'elif', 'else'}
[6,GLOBAL, ERROR]: Error occurred during parsing: abort
Traceback (most recent call last):
File "/opt/data/Izhikevich.py", line 10, in <module>
generate_nest_target(input_path="izhikevich.nestml",
File
"/usr/local/lib/python3.10/dist-packages/pynestml/frontend/pynestml_frontend.py",
line 229, in generate_nest_target
generate_target(input_path, target_platform="NEST", target_path=target_path,
logging_level=logging_level,
File
"/usr/local/lib/python3.10/dist-packages/pynestml/frontend/pynestml_frontend.py",
line 199, in generate_target
raise Exception("Error(s) occurred while processing the model")
Exception: Error(s) occurred while processing the model
which I do not understand. The syntaxis of nestml seems clear, no "end",
right? Then, what am I doing wrong?
Thanks!
gus.-
PS: I still have my doubts, as explained in the other thread, but I thought this is a
different issue... sorry if I did wrong!!!
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
9:43 p.m.
Thanks!!!!
This fixed it. However, there are some very minor incompatibilities between the tutorial
and the nestml code in 5.2.0, but nothing too complex. Now, I have it running and ready to
start the actual coding!
Thanks!
gus.-
14 Apr
14 Apr
7:05 p.m.
Dear Gustavo,
could you please elaborate more on those incompatibilities?
Or even better, create a pull request
<https://nest-simulator.readthedocs.io/en/v3.4/developer_space/workflows/development_workflow.html>
to fix them? That way, all users would benefit from your fixes. If you
need help for that, just let us know.
Many thanks and best regards,
Jochen!
On 13.04.23 21:43, gustavo.patow(a)udg.edu wrote:
Thanks!!!!
This fixed it. However, there are some very minor incompatibilities between the tutorial
and the nestml code in 5.2.0, but nothing too complex. Now, I have it running and ready to
start the actual coding!
Thanks!
gus.-
_______________________________________________
NEST Users mailing list --users(a)nest-simulator.org
To unsubscribe send an email tousers-leave(a)nest-simulator.org
--
Dr. Jochen Martin Eppler (he/him)
Simulation and Data Lab Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
---------------------------------------------------------------------
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.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens,
Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior
---------------------------------------------------------------------
8:22 p.m.
Dear Jochen,
The incompatibilities I mentioned are between the tutorial and the nestml version you
pointed me to:
https://github.com/nest/nestml/blob/v5.2.0/models/neurons/izhikevich.nestml
but all of them will disappear when the docker version and the latest nestml version are
the same. I mean, when no "end" commands are needed anymore in nestml...
In any case, it was renaming v -> V_m and u -> U_m, nothing really important!
;-)
cheers
gus.-
6:57 p.m.
Hi,
I've finally successfully recreated the Izhikevich tutorial, but when I try to run
the "homework" (i.e., generate the other results in the paper), I find some
strange results. Basically, every time I run the neuron with Simulate(), the new
simulation is ACCUMULATED after the previous result. I guess I should reset the voltmeter
between simulations somehow, but I couldn't find the adequate commend... Can you give
me any hint?
Second, I am doing the homework for this tutorial, reproducing the original results.
Should it suffice to enter the right values for a, b, c, and d? The results I am getting
do not look too similar to the ones in the paper, especially the bursts for the IB and CH
neurons... any idea?
cheers
gus.-
7:04 p.m.
Hi!
I've finally successfully recreated the Izhikevich
tutorial, but when I try to run the "homework" (i.e., generate the other results
in the paper), I find some strange results. Basically, every time I run the neuron with
Simulate(), the new simulation is ACCUMULATED after the previous result. I guess I should
reset the voltmeter between simulations somehow, but I couldn't find the adequate
commend... Can you give me any hint?
You can reset the data collected in the |voltmeter| by setting its
|n_events| field to 0 like so:
|vm = nest.Create("voltmeter") # create and connect neurons, simulate
vm.n_events = 0 # data from previous runs is gone |
For more information about the recording backend |memory|, see here:
https://nest-simulator.readthedocs.io/en/v3.4/models/recording_backend_memo…
More general information about recording from your simulations is here:
https://nest-simulator.readthedocs.io/en/v3.4/devices/record_from_simulatio…
Second, I am doing the homework for this tutorial,
reproducing the original results. Should it suffice to enter the right values for a, b, c,
and d? The results I am getting do not look too similar to the ones in the paper,
especially the bursts for the IB and CH neurons... any idea?
I am afraid, I’m not deep enough in the tutorial and can’t help you with
this one. One of my colleagues will have to pick this one up.
Cheers,
Jochen!
cheers
gus.-
_______________________________________________
NEST Users mailing list --users(a)nest-simulator.org
To unsubscribe send an email tousers-leave(a)nest-simulator.org
--
Dr. Jochen Martin Eppler (he/him)
Simulation and Data Lab Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
---------------------------------------------------------------------
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.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens,
Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior
---------------------------------------------------------------------
8:19 p.m.
Thanks, Jochen!!!
However, this does not completely solve the problem: now, for the second run of Simulate()
the simulation is empty until the end of the previous run, and then the second run starts.
I mean:
nest.Simulate(250) # -> generates a simulation from 0 to 250
vm.n_events = 0 # data from previous runs is gone
nest.Simulate(250). # -> This simulation goes from 250 to 500. It shows empty results
between 0 and 250 for V, and the actual simulation between 250 and 500 for V.
If we examine the voltmeter.events content after both runs, the entry 'times'
shows values between 250 and 500, so the command vm.n_events = 0 resets the contents (I
checked it), but NOT some internal time counter.
Should I do a full nest.ResetKernel() and rebuilt everything (i.e., the network) for EACH
run? No problem, although it sounds strange to me... ;-)
in any case, thanks again!!!
gus.-
11:32 p.m.
Hi!
However, this does not completely solve the problem:
now, for the second run of Simulate() the simulation is empty until the end of the
previous run, and then the second run starts. I mean:
nest.Simulate(250) # -> generates a simulation from 0 to 250
vm.n_events = 0 # data from previous runs is gone
nest.Simulate(250). # -> This simulation goes from 250 to 500. It shows empty results
between 0 and 250 for V, and the actual simulation between 250 and 500 for V.
If we examine the voltmeter.events content after both runs, the entry 'times'
shows values between 250 and 500, so the command vm.n_events = 0 resets the contents (I
checked it), but NOT some internal time counter.
Indeed. The setting I gave you only removes the events from the
/specific/ device you’re using it on. Nothing else.
You can also reset time by calling |nest.biological_time = 0|. However,
that comes with a big fat warning message printed to your screen for
good reasons.
Should I do a full nest.ResetKernel() and rebuilt
everything (i.e., the network) for EACH run? No problem, although it sounds strange to
me... ;-)
Short answer: Yes. This is what you should do.
There is an ongoing discussion
<https://github.com/nest/nest-simulator/issues/2337> about resetting the
/network state/ instead of completely destroying it (i.e. using
|ResetKernel|) and rebuilding it. A short summary for why we don’t
support that is that if you ask four people what a hypothetical
|ResetNetwork| function should do, you probably get five different
opinions and is extremely hard to track and reset each and every
variable involved in the simulation and it is not even clear to what
they should be reset to. Also see #1919
<https://github.com/nest/nest-simulator/pull/1919> and the example
|pynest/examples/store_restore_network.py| that resulted from it.
Cheers,
Jochen!
--
Dr. Jochen Martin Eppler (he/him)
Simulation and Data Lab Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
---------------------------------------------------------------------
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.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens,
Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior
---------------------------------------------------------------------
15 Apr
15 Apr
1:26 p.m.
Dear Jochen,
I have switched to a full network reset with ResetKernel(), and it WORKS like a
charm!!!
Not only that but now I was able to approximately reproduce ALL plots in the famous
figure from Izhikevich's paper!! GREAT!!!
Now, I will set out to implement my original target, the paper by Chen and Campbell:
Chen, L., Campbell, S.A. Exact mean-field models for spiking neural networks with
adaptation. J Comput Neurosci 50, 445–469 (2022).
https://doi.org/10.1007/s10827-022-00825-9
Thank you very much for all your invaluable help!!!
cheers
gus.-
379
days inactive
382
days old
9 comments
3 participants
participants (3)
-
Babu, Pooja -
gustavo.patow＠udg.edu -
Jochen Martin Eppler