13 Jun
2024
13 Jun
'24
10:59 a.m.
I was using an old version of nest (3.5) and nestml. Someone sent me a nestml model, and
that worked. I wanted to make my own model, but the tutorials had a different format. In
particular, it seems like the first line of code in the tutorials start with model, and
the old version started with neuron of synapse.
So, I thought it was time to upgrade, so installed nest 3.7, and pip-ed nestml. (I also
installed PyNN as that's the way I typically work.) When I imported generate_target
(through python 3.12), I got the typical PyGSL warning; I think that's because I'm
using python 3.12 not 3.11, and I don't think it matters in this case.
Then I ran the generate_target and I got an error mismatched input 'model'
expecting {newline, 'neuron', 'synapse}
I expect there's something like a yacc table that specifies the syntax, and somehow
I've got the old syntax.
I've tried it with several version of nestml 7.0.2, 7.0.0, 6.0.0 and 5.0.0. I think
5.0.0 had the old syntax. I've tried several models from the library, and the
Izhikevich tutorial.
Any thoughts about how to fix it?
-Chris
11:34 a.m.
That's exactly what I'm trying to do. I merely want to load one of the modules
from the website Models library - NESTML documentation 1.0.0
documentation<https://nestml.readthedocs.io/en/latest/models_library/index.html>.
For example, I tried the hill_tononi_neuron. When I try generate_target, I get the
mismatched input 'model' expecting {newline, 'neuron', 'synapse}
error. I get a different code generation error if I change model to neuron. I used the
newest nestml version (7.0.2) for some time. I'm currently on 7.0.0, but it's easy
enough to change back.
-Chris
From: thanh-binh.to(a)online.de <thanh-binh.to(a)online.de>
Sent: 13 June 2024 10:11
To: NEST User Mailing List <users(a)nest-simulator.org>
Subject: [NEST Users] Re: nestml syntax problem
You don't often get email from
thanh-binh.to@online.de<mailto:thanh-binh.to@online.de>. Learn why this is
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Personal I'd like to recommend you to use the newest version of Nestml and to adapt
your old neuron model to the new syntax.
For doing it you have to compare a nestml model of any neuron in the current nestml
version to the old one.
Normally you have to put a word "end" at the end of each segment in model
Hope that help
BR Binh
Gesendet mit der mobilen Mail App
Am 13.06.24 um 10:59 schrieb Chris Huyck
Von: "Chris Huyck" <C.Huyck@mdx.ac.uk<mailto:C.Huyck@mdx.ac.uk>>
Datum: 13. Juni 2024
An: "NEST User Mailing List"
<users@nest-simulator.org<mailto:users@nest-simulator.org>>
Cc:
Betreff: [NEST Users] nestml syntax problem
I was using an old version of nest (3.5) and nestml. Someone sent me a nestml model, and
that worked. I wanted to make my own model, but the tutorials had a different format. In
particular, it seems like the first line of code in the tutorials start with model, and
the old version started with neuron of synapse.
So, I thought it was time to upgrade, so installed nest 3.7, and pip-ed nestml. (I also
installed PyNN as that's the way I typically work.) When I imported generate_target
(through python 3.12), I got the typical PyGSL warning; I think that's because I'm
using python 3.12 not 3.11, and I don't think it matters in this case.
Then I ran the generate_target and I got an error mismatched input 'model'
expecting {newline, 'neuron', 'synapse}
I expect there's something like a yacc table that specifies the syntax, and somehow
I've got the old syntax.
I've tried it with several version of nestml 7.0.2, 7.0.0, 6.0.0 and 5.0.0. I think
5.0.0 had the old syntax. I've tried several models from the library, and the
Izhikevich tutorial.
Any thoughts about how to fix it?
-Chris
11:40 a.m.
Hello Chris,
The latest release of NESTML (v7.0.2) uses the “neuron” or “synapse” at the beginning of
the model definition. We have unified this in our latest changes to the language where
they are replaced by “model”, however, this is not yet released.
It looks like you have conflicting versions of NESTML installed. I would suggest you
uninstall all the old NESTML instances and install it again via pip.
The pip-installed version should have models that begin with either “neuron” or “synapse”.
The corresponding grammar can be found here:
https://github.com/nest/nestml/tree/v7.0.2/pynestml/grammars
Apologies for the confusion. We are in the process of doing a pre-release of the new
language changes soon.
Hope this helps!
Best regards,
Pooja
On 13. Jun 2024, at 11:11, thanh-binh.to(a)online.de
wrote:
Personal I‘d like to recommend you to use the newest version of Nestml and to adapt your
old neuron model to the new syntax.
For doing it you have to compare a nestml model of any neuron in the current nestml
version to the old one.
Normally you have to put a word “end” at the end of each segment in model
Hope that help
BR Binh
Gesendet mit der mobilen Mail App
Am 13.06.24 um 10:59 schrieb Chris Huyck
Von: "Chris Huyck" <C.Huyck(a)mdx.ac.uk <mailto:C.Huyck@mdx.ac.uk>>
Datum: 13. Juni 2024
An: "NEST User Mailing List" <users(a)nest-simulator.org
<mailto:users@nest-simulator.org>>
Cc:
Betreff: [NEST Users] nestml syntax problem
I was using an old version of nest (3.5) and nestml. Someone sent me a nestml model, and
that worked. I wanted to make my own model, but the tutorials had a different format. In
particular, it seems like the first line of code in the tutorials start with model, and
the old version started with neuron of synapse.
So, I thought it was time to upgrade, so installed nest 3.7, and pip-ed nestml. (I also
installed PyNN as that's the way I typically work.) When I imported generate_target
(through python 3.12), I got the typical PyGSL warning; I think that's because I'm
using python 3.12 not 3.11, and I don't think it matters in this case.
Then I ran the generate_target and I got an error mismatched input 'model'
expecting {newline, 'neuron', 'synapse}
I expect there's something like a yacc table that specifies the syntax, and somehow
I've got the old syntax.
I've tried it with several version of nestml 7.0.2, 7.0.0, 6.0.0 and 5.0.0. I think
5.0.0 had the old syntax. I've tried several models from the library, and the
Izhikevich tutorial.
Any thoughts about how to fix it?
-Chris
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
11:55 a.m.
Hello Pooja,
Firstly, thanks for the quick response.
I've taken the hill_tononi_neuron model from Models library - NESTML documentation
1.0.0
documentation<https://nestml.readthedocs.io/en/latest/models_library/index.html>,
and it gives me the an error mismatched input 'model' expecting {newline,
'neuron', 'synapse}. I change model to neuron in the .nestml file, and I get
an extraneous input 'onCondition' error. If I try with izhekivich_task.nestml
from
raw.githubusercontent.com/nest/nestml/master/doc/tutorials/izhikevich/izhik…
I get the 'model' error; if I change model to neuron I get an extraneous input
'onRecieve' error. Are there any working models in nestml 7.0.2 that work?
-Chris
From: Babu, Pooja <p.babu(a)fz-juelich.de>
Sent: 13 June 2024 10:40
To: NEST User Mailing List <users(a)nest-simulator.org>
Subject: [NEST Users] Re: nestml syntax problem
You don't often get email from
p.babu@fz-juelich.de<mailto:p.babu@fz-juelich.de>. Learn why this is
important<https://aka.ms/LearnAboutSenderIdentification>
Hello Chris,
The latest release of NESTML (v7.0.2) uses the "neuron" or "synapse"
at the beginning of the model definition. We have unified this in our latest changes to
the language where they are replaced by "model", however, this is not yet
released.
It looks like you have conflicting versions of NESTML installed. I would suggest you
uninstall all the old NESTML instances and install it again via pip.
The pip-installed version should have models that begin with either "neuron" or
"synapse". The corresponding grammar can be found here:
https://github.com/nest/nestml/tree/v7.0.2/pynestml/grammars
Apologies for the confusion. We are in the process of doing a pre-release of the new
language changes soon.
Hope this helps!
Best regards,
Pooja
On 13. Jun 2024, at 11:11, thanh-binh.to@online.de<mailto:thanh-binh.to@online.de>
wrote:
Personal I'd like to recommend you to use the newest version of Nestml and to adapt
your old neuron model to the new syntax.
For doing it you have to compare a nestml model of any neuron in the current nestml
version to the old one.
Normally you have to put a word "end" at the end of each segment in model
Hope that help
BR Binh
Gesendet mit der mobilen Mail App
Am 13.06.24 um 10:59 schrieb Chris Huyck
Von: "Chris Huyck" <C.Huyck@mdx.ac.uk<mailto:C.Huyck@mdx.ac.uk>>
Datum: 13. Juni 2024
An: "NEST User Mailing List"
<users@nest-simulator.org<mailto:users@nest-simulator.org>>
Cc:
Betreff: [NEST Users] nestml syntax problem
I was using an old version of nest (3.5) and nestml. Someone sent me a nestml model, and
that worked. I wanted to make my own model, but the tutorials had a different format. In
particular, it seems like the first line of code in the tutorials start with model, and
the old version started with neuron of synapse.
So, I thought it was time to upgrade, so installed nest 3.7, and pip-ed nestml. (I also
installed PyNN as that's the way I typically work.) When I imported generate_target
(through python 3.12), I got the typical PyGSL warning; I think that's because I'm
using python 3.12 not 3.11, and I don't think it matters in this case.
Then I ran the generate_target and I got an error mismatched input 'model'
expecting {newline, 'neuron', 'synapse}
I expect there's something like a yacc table that specifies the syntax, and somehow
I've got the old syntax.
I've tried it with several version of nestml 7.0.2, 7.0.0, 6.0.0 and 5.0.0. I think
5.0.0 had the old syntax. I've tried several models from the library, and the
Izhikevich tutorial.
Any thoughts about how to fix it?
-Chris
_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
12:15 p.m.
Hi Chris,
The keywords “model”, “OnCondition” and “OnReceieve” are all the new changes to the NESTML
language which is not yet released.
As I mentioned earlier, it looks like you have the NESTML 7.0.2 installed, but the model
files you are using are the new ones with the language updates. The “hill_tonini” model
corresponding to your version should be:
https://github.com/nest/nestml/blob/v7.0.2/models/neurons/hill_tononi.nestml
We will fix the documentation to point to the "release version" to avoid further
confusion.
Regards,
Pooja
On 13. Jun 2024, at 11:55, Chris Huyck
<C.Huyck(a)mdx.ac.uk> wrote:
Hello Pooja,
Firstly, thanks for the quick response.
I’ve taken the hill_tononi_neuron model from Models library — NESTML documentation 1.0.0
documentation <https://nestml.readthedocs.io/en/latest/models_library/index.html>,
and it gives me the an error mismatched input 'model' expecting {newline,
'neuron', 'synapse}. I change model to neuron in the .nestml file, and I get
an extraneous input ‘onCondition’ error. If I try with izhekivich_task.nestml
fromraw.githubusercontent.com/nest/nestml/master/doc/tutorials/izhikevich/i…
<https://raw.githubusercontent.com/nest/nestml/master/doc/tutorials/izhikevich/izhikevich_task.nestml>
I get the ‘model’ error; if I change model to neuron I get an extraneous input
‘onRecieve’ error. Are there any working models in nestml 7.0.2 that work?
-Chris
From: Babu, Pooja <p.babu(a)fz-juelich.de <mailto:p.babu@fz-juelich.de>>
Sent: 13 June 2024 10:40
To: NEST User Mailing List <users(a)nest-simulator.org
<mailto:users@nest-simulator.org>>
Subject: [NEST Users] Re: nestml syntax problem
You don't often get email from p.babu(a)fz-juelich.de
<mailto:p.babu@fz-juelich.de>. Learn why this is important
<https://aka.ms/LearnAboutSenderIdentification>
Hello Chris,
The latest release of NESTML (v7.0.2) uses the “neuron” or “synapse” at the beginning of
the model definition. We have unified this in our latest changes to the language where
they are replaced by “model”, however, this is not yet released.
It looks like you have conflicting versions of NESTML installed. I would suggest you
uninstall all the old NESTML instances and install it again via pip.
The pip-installed version should have models that begin with either “neuron” or
“synapse”. The corresponding grammar can be found here:
https://github.com/nest/nestml/tree/v7.0.2/pynestml/grammars
Apologies for the confusion. We are in the process of doing a pre-release of the new
language changes soon.
Hope this helps!
Best regards,
Pooja
On 13. Jun 2024, at 11:11, thanh-binh.to(a)online.de <mailto:thanh-binh.to@online.de>
wrote:
Personal I‘d like to recommend you to use the newest version of Nestml and to adapt your
old neuron model to the new syntax.
For doing it you have to compare a nestml model of any neuron in the current nestml
version to the old one.
Normally you have to put a word “end” at the end of each segment in model
Hope that help
BR Binh
Gesendet mit der mobilen Mail App
Am 13.06.24 um 10:59 schrieb Chris Huyck
Von: "Chris Huyck" <C.Huyck(a)mdx.ac.uk <mailto:C.Huyck@mdx.ac.uk>>
Datum: 13. Juni 2024
An: "NEST User Mailing List" <users(a)nest-simulator.org
<mailto:users@nest-simulator.org>>
Cc:
Betreff: [NEST Users] nestml syntax problem
I was using an old version of nest (3.5) and nestml. Someone sent me a nestml model, and
that worked. I wanted to make my own model, but the tutorials had a different format. In
particular, it seems like the first line of code in the tutorials start with model, and
the old version started with neuron of synapse.
So, I thought it was time to upgrade, so installed nest 3.7, and pip-ed nestml. (I also
installed PyNN as that's the way I typically work.) When I imported generate_target
(through python 3.12), I got the typical PyGSL warning; I think that's because I'm
using python 3.12 not 3.11, and I don't think it matters in this case.
Then I ran the generate_target and I got an error mismatched input 'model'
expecting {newline, 'neuron', 'synapse}
I expect there's something like a yacc table that specifies the syntax, and somehow
I've got the old syntax.
I've tried it with several version of nestml 7.0.2, 7.0.0, 6.0.0 and 5.0.0. I think
5.0.0 had the old syntax. I've tried several models from the library, and the
Izhikevich tutorial.
Any thoughts about how to fix it?
-Chris
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
<mailto:users@nest-simulator.org>
To unsubscribe send an email to users-leave(a)nest-simulator.org
<mailto:users-leave@nest-simulator.org>
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
5:34 p.m.
This was a pretty straight forward solution. I used the hill_tononi.nestml file below,
and nestml ran and compiled. The nest.Install works, but I can't actually run the
model. I'll try to sort that out.
So, thanks!
-Chris
From: Babu, Pooja <p.babu(a)fz-juelich.de>
Sent: 13 June 2024 11:15
To: NEST User Mailing List <users(a)nest-simulator.org>
Subject: [NEST Users] Re: nestml syntax problem
Hi Chris,
The keywords "model", "OnCondition" and "OnReceieve" are all
the new changes to the NESTML language which is not yet released.
As I mentioned earlier, it looks like you have the NESTML 7.0.2 installed, but the model
files you are using are the new ones with the language updates. The
"hill_tonini" model corresponding to your version should be:
https://github.com/nest/nestml/blob/v7.0.2/models/neurons/hill_tononi.nestml
We will fix the documentation to point to the "release version" to avoid further
confusion.
Regards,
Pooja
On 13. Jun 2024, at 11:55, Chris Huyck
<C.Huyck@mdx.ac.uk<mailto:C.Huyck@mdx.ac.uk>> wrote:
Hello Pooja,
Firstly, thanks for the quick response.
I've taken the hill_tononi_neuron model from Models library - NESTML documentation
1.0.0
documentation<https://nestml.readthedocs.io/en/latest/models_library/index.html>,
and it gives me the an error mismatched input 'model' expecting {newline,
'neuron', 'synapse}. I change model to neuron in the .nestml file, and I get
an extraneous input 'onCondition' error. If I try with izhekivich_task.nestml
fromraw.githubusercontent.com/nest/nestml/master/doc/tutorials/izhikevich/i…
I get the 'model' error; if I change model to neuron I get an extraneous input
'onRecieve' error. Are there any working models in nestml 7.0.2 that work?
-Chris
From: Babu, Pooja <p.babu@fz-juelich.de<mailto:p.babu@fz-juelich.de>>
Sent: 13 June 2024 10:40
To: NEST User Mailing List
<users@nest-simulator.org<mailto:users@nest-simulator.org>>
Subject: [NEST Users] Re: nestml syntax problem
You don't often get email from
p.babu@fz-juelich.de<mailto:p.babu@fz-juelich.de>. Learn why this is
important<https://aka.ms/LearnAboutSenderIdentification>
Hello Chris,
The latest release of NESTML (v7.0.2) uses the "neuron" or "synapse"
at the beginning of the model definition. We have unified this in our latest changes to
the language where they are replaced by "model", however, this is not yet
released.
It looks like you have conflicting versions of NESTML installed. I would suggest you
uninstall all the old NESTML instances and install it again via pip.
The pip-installed version should have models that begin with either "neuron" or
"synapse". The corresponding grammar can be found here:
https://github.com/nest/nestml/tree/v7.0.2/pynestml/grammars
Apologies for the confusion. We are in the process of doing a pre-release of the new
language changes soon.
Hope this helps!
Best regards,
Pooja
On 13. Jun 2024, at 11:11, thanh-binh.to@online.de<mailto:thanh-binh.to@online.de>
wrote:
Personal I'd like to recommend you to use the newest version of Nestml and to adapt
your old neuron model to the new syntax.
For doing it you have to compare a nestml model of any neuron in the current nestml
version to the old one.
Normally you have to put a word "end" at the end of each segment in model
Hope that help
BR Binh
Gesendet mit der mobilen Mail App
Am 13.06.24 um 10:59 schrieb Chris Huyck
Von: "Chris Huyck" <C.Huyck@mdx.ac.uk<mailto:C.Huyck@mdx.ac.uk>>
Datum: 13. Juni 2024
An: "NEST User Mailing List"
<users@nest-simulator.org<mailto:users@nest-simulator.org>>
Cc:
Betreff: [NEST Users] nestml syntax problem
I was using an old version of nest (3.5) and nestml. Someone sent me a nestml model, and
that worked. I wanted to make my own model, but the tutorials had a different format. In
particular, it seems like the first line of code in the tutorials start with model, and
the old version started with neuron of synapse.
So, I thought it was time to upgrade, so installed nest 3.7, and pip-ed nestml. (I also
installed PyNN as that's the way I typically work.) When I imported generate_target
(through python 3.12), I got the typical PyGSL warning; I think that's because I'm
using python 3.12 not 3.11, and I don't think it matters in this case.
Then I ran the generate_target and I got an error mismatched input 'model'
expecting {newline, 'neuron', 'synapse}
I expect there's something like a yacc table that specifies the syntax, and somehow
I've got the old syntax.
I've tried it with several version of nestml 7.0.2, 7.0.0, 6.0.0 and 5.0.0. I think
5.0.0 had the old syntax. I've tried several models from the library, and the
Izhikevich tutorial.
Any thoughts about how to fix it?
-Chris
_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
19 Jun
19 Jun
10:58 a.m.
I seem to be having problems with pyNN accessing the new model. I should note that the
first problem is that all of the 7.0.2 nesml models are already in the standard nest. So,
it's not clear, which version one is using. So, I switched to the ignore_and_fire
model, but changed the name to ignore_and_spike. A simple change of file name and model
name was sufficient. I got that running in pyNest. (It's a really simple model to
work with.)
I can also get it running in pyNN, but I can't use the Setup. If I do, it changes
something and I no longer have access to ignore_and_spike model. I'm using pyNN
0.12.3.
-Chris
From: Chris Huyck
Sent: 13 June 2024 16:34
To: NEST User Mailing List <users(a)nest-simulator.org>
Subject: RE: [NEST Users] Re: nestml syntax problem
This was a pretty straight forward solution. I used the hill_tononi.nestml file below,
and nestml ran and compiled. The nest.Install works, but I can't actually run the
model. I'll try to sort that out.
So, thanks!
-Chris
From: Babu, Pooja <p.babu@fz-juelich.de<mailto:p.babu@fz-juelich.de>>
Sent: 13 June 2024 11:15
To: NEST User Mailing List
<users@nest-simulator.org<mailto:users@nest-simulator.org>>
Subject: [NEST Users] Re: nestml syntax problem
Hi Chris,
The keywords "model", "OnCondition" and "OnReceieve" are all
the new changes to the NESTML language which is not yet released.
As I mentioned earlier, it looks like you have the NESTML 7.0.2 installed, but the model
files you are using are the new ones with the language updates. The
"hill_tonini" model corresponding to your version should be:
https://github.com/nest/nestml/blob/v7.0.2/models/neurons/hill_tononi.nestml
We will fix the documentation to point to the "release version" to avoid further
confusion.
Regards,
Pooja
On 13. Jun 2024, at 11:55, Chris Huyck
<C.Huyck@mdx.ac.uk<mailto:C.Huyck@mdx.ac.uk>> wrote:
Hello Pooja,
Firstly, thanks for the quick response.
I've taken the hill_tononi_neuron model from Models library - NESTML documentation
1.0.0
documentation<https://nestml.readthedocs.io/en/latest/models_library/index.html>,
and it gives me the an error mismatched input 'model' expecting {newline,
'neuron', 'synapse}. I change model to neuron in the .nestml file, and I get
an extraneous input 'onCondition' error. If I try with izhekivich_task.nestml
fromraw.githubusercontent.com/nest/nestml/master/doc/tutorials/izhikevich/i…
I get the 'model' error; if I change model to neuron I get an extraneous input
'onRecieve' error. Are there any working models in nestml 7.0.2 that work?
-Chris
From: Babu, Pooja <p.babu@fz-juelich.de<mailto:p.babu@fz-juelich.de>>
Sent: 13 June 2024 10:40
To: NEST User Mailing List
<users@nest-simulator.org<mailto:users@nest-simulator.org>>
Subject: [NEST Users] Re: nestml syntax problem
You don't often get email from
p.babu@fz-juelich.de<mailto:p.babu@fz-juelich.de>. Learn why this is
important<https://aka.ms/LearnAboutSenderIdentification>
Hello Chris,
The latest release of NESTML (v7.0.2) uses the "neuron" or "synapse"
at the beginning of the model definition. We have unified this in our latest changes to
the language where they are replaced by "model", however, this is not yet
released.
It looks like you have conflicting versions of NESTML installed. I would suggest you
uninstall all the old NESTML instances and install it again via pip.
The pip-installed version should have models that begin with either "neuron" or
"synapse". The corresponding grammar can be found here:
https://github.com/nest/nestml/tree/v7.0.2/pynestml/grammars
Apologies for the confusion. We are in the process of doing a pre-release of the new
language changes soon.
Hope this helps!
Best regards,
Pooja
On 13. Jun 2024, at 11:11, thanh-binh.to@online.de<mailto:thanh-binh.to@online.de>
wrote:
Personal I'd like to recommend you to use the newest version of Nestml and to adapt
your old neuron model to the new syntax.
For doing it you have to compare a nestml model of any neuron in the current nestml
version to the old one.
Normally you have to put a word "end" at the end of each segment in model
Hope that help
BR Binh
Gesendet mit der mobilen Mail App
Am 13.06.24 um 10:59 schrieb Chris Huyck
Von: "Chris Huyck" <C.Huyck@mdx.ac.uk<mailto:C.Huyck@mdx.ac.uk>>
Datum: 13. Juni 2024
An: "NEST User Mailing List"
<users@nest-simulator.org<mailto:users@nest-simulator.org>>
Cc:
Betreff: [NEST Users] nestml syntax problem
I was using an old version of nest (3.5) and nestml. Someone sent me a nestml model, and
that worked. I wanted to make my own model, but the tutorials had a different format. In
particular, it seems like the first line of code in the tutorials start with model, and
the old version started with neuron of synapse.
So, I thought it was time to upgrade, so installed nest 3.7, and pip-ed nestml. (I also
installed PyNN as that's the way I typically work.) When I imported generate_target
(through python 3.12), I got the typical PyGSL warning; I think that's because I'm
using python 3.12 not 3.11, and I don't think it matters in this case.
Then I ran the generate_target and I got an error mismatched input 'model'
expecting {newline, 'neuron', 'synapse}
I expect there's something like a yacc table that specifies the syntax, and somehow
I've got the old syntax.
I've tried it with several version of nestml 7.0.2, 7.0.0, 6.0.0 and 5.0.0. I think
5.0.0 had the old syntax. I've tried several models from the library, and the
Izhikevich tutorial.
Any thoughts about how to fix it?
-Chris
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1:29 p.m.
Hello Chris,
If you want to generate the neuron models which has the same name in NEST, you can use the
“suffix” option in the “generate_nest_target” function. This adds the suffix to the model
name during code generation.
For example:
generate_nest_target(input_path=“test_model.nestml",
target_path="target",
logging_level="INFO",
suffix=“_nestml”)
nest.Install(“nestmlmodule”)
n = nest.Create(“test_model_nestml”)
We do not currently provide pyNN support for NESTML models. If you manage to run NESTML
models in pyNN, do let us know.
Regards,
Pooja
On 19. Jun 2024, at 10:58, Chris Huyck
<C.Huyck(a)mdx.ac.uk> wrote:
I seem to be having problems with pyNN accessing the new model. I should note that the
first problem is that all of the 7.0.2 nesml models are already in the standard nest. So,
it’s not clear, which version one is using. So, I switched to the ignore_and_fire model,
but changed the name to ignore_and_spike. A simple change of file name and model name was
sufficient. I got that running in pyNest. (It’s a really simple model to work with.)
I can also get it running in pyNN, but I can’t use the Setup. If I do, it changes
something and I no longer have access to ignore_and_spike model. I’m using pyNN 0.12.3.
-Chris
From: Chris Huyck
Sent: 13 June 2024 16:34
To: NEST User Mailing List <users(a)nest-simulator.org>
Subject: RE: [NEST Users] Re: nestml syntax problem
This was a pretty straight forward solution. I used the hill_tononi.nestml file below,
and nestml ran and compiled. The nest.Install works, but I can’t actually run the model.
I’ll try to sort that out.
So, thanks!
-Chris
From: Babu, Pooja <p.babu(a)fz-juelich.de <mailto:p.babu@fz-juelich.de>>
Sent: 13 June 2024 11:15
To: NEST User Mailing List <users(a)nest-simulator.org
<mailto:users@nest-simulator.org>>
Subject: [NEST Users] Re: nestml syntax problem
Hi Chris,
The keywords “model”, “OnCondition” and “OnReceieve” are all the new changes to the
NESTML language which is not yet released.
As I mentioned earlier, it looks like you have the NESTML 7.0.2 installed, but the model
files you are using are the new ones with the language updates. The “hill_tonini” model
corresponding to your version should be:
https://github.com/nest/nestml/blob/v7.0.2/models/neurons/hill_tononi.nestml
We will fix the documentation to point to the "release version" to avoid
further confusion.
Regards,
Pooja
On 13. Jun 2024, at 11:55, Chris Huyck <C.Huyck(a)mdx.ac.uk
<mailto:C.Huyck@mdx.ac.uk>> wrote:
Hello Pooja,
Firstly, thanks for the quick response.
I’ve taken the hill_tononi_neuron model from Models library — NESTML documentation 1.0.0
documentation <https://nestml.readthedocs.io/en/latest/models_library/index.html>,
and it gives me the an error mismatched input 'model' expecting {newline,
'neuron', 'synapse}. I change model to neuron in the .nestml file, and I get
an extraneous input ‘onCondition’ error. If I try with izhekivich_task.nestml
fromraw.githubusercontent.com/nest/nestml/master/doc/tutorials/izhikevich/i…
<https://raw.githubusercontent.com/nest/nestml/master/doc/tutorials/izhikevich/izhikevich_task.nestml>
I get the ‘model’ error; if I change model to neuron I get an extraneous input
‘onRecieve’ error. Are there any working models in nestml 7.0.2 that work?
-Chris
From: Babu, Pooja <p.babu(a)fz-juelich.de <mailto:p.babu@fz-juelich.de>>
Sent: 13 June 2024 10:40
To: NEST User Mailing List <users(a)nest-simulator.org
<mailto:users@nest-simulator.org>>
Subject: [NEST Users] Re: nestml syntax problem
You don't often get email from p.babu(a)fz-juelich.de
<mailto:p.babu@fz-juelich.de>. Learn why this is important
<https://aka.ms/LearnAboutSenderIdentification>
Hello Chris,
The latest release of NESTML (v7.0.2) uses the “neuron” or “synapse” at the beginning of
the model definition. We have unified this in our latest changes to the language where
they are replaced by “model”, however, this is not yet released.
It looks like you have conflicting versions of NESTML installed. I would suggest you
uninstall all the old NESTML instances and install it again via pip.
The pip-installed version should have models that begin with either “neuron” or
“synapse”. The corresponding grammar can be found here:
https://github.com/nest/nestml/tree/v7.0.2/pynestml/grammars
Apologies for the confusion. We are in the process of doing a pre-release of the new
language changes soon.
Hope this helps!
Best regards,
Pooja
On 13. Jun 2024, at 11:11, thanh-binh.to(a)online.de <mailto:thanh-binh.to@online.de>
wrote:
Personal I‘d like to recommend you to use the newest version of Nestml and to adapt your
old neuron model to the new syntax.
For doing it you have to compare a nestml model of any neuron in the current nestml
version to the old one.
Normally you have to put a word “end” at the end of each segment in model
Hope that help
BR Binh
Gesendet mit der mobilen Mail App
Am 13.06.24 um 10:59 schrieb Chris Huyck
Von: "Chris Huyck" <C.Huyck(a)mdx.ac.uk <mailto:C.Huyck@mdx.ac.uk>>
Datum: 13. Juni 2024
An: "NEST User Mailing List" <users(a)nest-simulator.org
<mailto:users@nest-simulator.org>>
Cc:
Betreff: [NEST Users] nestml syntax problem
I was using an old version of nest (3.5) and nestml. Someone sent me a nestml model, and
that worked. I wanted to make my own model, but the tutorials had a different format. In
particular, it seems like the first line of code in the tutorials start with model, and
the old version started with neuron of synapse.
So, I thought it was time to upgrade, so installed nest 3.7, and pip-ed nestml. (I also
installed PyNN as that's the way I typically work.) When I imported generate_target
(through python 3.12), I got the typical PyGSL warning; I think that's because I'm
using python 3.12 not 3.11, and I don't think it matters in this case.
Then I ran the generate_target and I got an error mismatched input 'model'
expecting {newline, 'neuron', 'synapse}
I expect there's something like a yacc table that specifies the syntax, and somehow
I've got the old syntax.
I've tried it with several version of nestml 7.0.2, 7.0.0, 6.0.0 and 5.0.0. I think
5.0.0 had the old syntax. I've tried several models from the library, and the
Izhikevich tutorial.
Any thoughts about how to fix it?
-Chris
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
<mailto:users@nest-simulator.org>
To unsubscribe send an email to users-leave(a)nest-simulator.org
<mailto:users-leave@nest-simulator.org>
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<mailto:users@nest-simulator.org>
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To unsubscribe send an email to users-leave(a)nest-simulator.org
2:25 p.m.
Thanks Pooja.
My problem was loading a nestml generated neural model into PyNN. In particular, the
problem is loading into PyNN and then executing the simulation in nest. (It seems one of
the benefits of nestML is that it generates code for SpiNNaker, and I hope to try that
eventually.)
From python I
import pyNN.nest as sim
from pyNN.nest import native_cell_type
igSpike_neuron = native_cell_type('ignore_and_spike')
cells=sim.Population(2,igSpike_neuron,{})
sim.run(100.0)
#the model gives two emited spike
sim.setup(timestep=1.0)
cells=sim.Population(2,igSpike_neuron,{})
#the error output culminating with....
#error File
"/home/christian3/CAs/jun24/nest-simulator-3.7/nest-install/lib/python3.12/site-packages/nest/ll_api.py",
line 103, in catching_sli_run
# raise exceptionCls(commandname, message)
#nest.lib.hl_api_exceptions.NESTErrors.UnknownComponent: UnknownComponent in SLI function
GetDefaults_l: /ignore_and_spike is not a known component.
So, it loads the model properly, and runs it. However, when I do a setup, it no longer
recognises ignore_and_spike. (Almost all of my existing scripts use setup.)
The name of the model wasn't my problem. The name of model is easy to modify as I did.
(I am sure your answer about that is correct, though I haven't tried it.)
-Chris
From: Babu, Pooja <p.babu(a)fz-juelich.de>
Sent: 19 June 2024 12:29
To: NEST User Mailing List <users(a)nest-simulator.org>
Subject: [NEST Users] Re: nestml syntax problem
Hello Chris,
If you want to generate the neuron models which has the same name in NEST, you can use the
"suffix" option in the "generate_nest_target" function. This adds the
suffix to the model name during code generation.
For example:
generate_nest_target(input_path="test_model.nestml",
target_path="target",
logging_level="INFO",
suffix="_nestml")
nest.Install("nestmlmodule")
n = nest.Create("test_model_nestml")
We do not currently provide pyNN support for NESTML models. If you manage to run NESTML
models in pyNN, do let us know.
Regards,
Pooja
On 19. Jun 2024, at 10:58, Chris Huyck
<C.Huyck@mdx.ac.uk<mailto:C.Huyck@mdx.ac.uk>> wrote:
I seem to be having problems with pyNN accessing the new model. I should note that the
first problem is that all of the 7.0.2 nesml models are already in the standard nest. So,
it's not clear, which version one is using. So, I switched to the ignore_and_fire
model, but changed the name to ignore_and_spike. A simple change of file name and model
name was sufficient. I got that running in pyNest. (It's a really simple model to
work with.)
I can also get it running in pyNN, but I can't use the Setup. If I do, it changes
something and I no longer have access to ignore_and_spike model. I'm using pyNN
0.12.3.
-Chris
From: Chris Huyck
Sent: 13 June 2024 16:34
To: NEST User Mailing List
<users@nest-simulator.org<mailto:users@nest-simulator.org>>
Subject: RE: [NEST Users] Re: nestml syntax problem
This was a pretty straight forward solution. I used the hill_tononi.nestml file below,
and nestml ran and compiled. The nest.Install works, but I can't actually run the
model. I'll try to sort that out.
So, thanks!
-Chris
From: Babu, Pooja <p.babu@fz-juelich.de<mailto:p.babu@fz-juelich.de>>
Sent: 13 June 2024 11:15
To: NEST User Mailing List
<users@nest-simulator.org<mailto:users@nest-simulator.org>>
Subject: [NEST Users] Re: nestml syntax problem
Hi Chris,
The keywords "model", "OnCondition" and "OnReceieve" are all
the new changes to the NESTML language which is not yet released.
As I mentioned earlier, it looks like you have the NESTML 7.0.2 installed, but the model
files you are using are the new ones with the language updates. The
"hill_tonini" model corresponding to your version should be:
https://github.com/nest/nestml/blob/v7.0.2/models/neurons/hill_tononi.nestml
We will fix the documentation to point to the "release version" to avoid further
confusion.
Regards,
Pooja
On 13. Jun 2024, at 11:55, Chris Huyck
<C.Huyck@mdx.ac.uk<mailto:C.Huyck@mdx.ac.uk>> wrote:
Hello Pooja,
Firstly, thanks for the quick response.
I've taken the hill_tononi_neuron model from Models library - NESTML documentation
1.0.0
documentation<https://nestml.readthedocs.io/en/latest/models_library/index.html>,
and it gives me the an error mismatched input 'model' expecting {newline,
'neuron', 'synapse}. I change model to neuron in the .nestml file, and I get
an extraneous input 'onCondition' error. If I try with izhekivich_task.nestml
fromraw.githubusercontent.com/nest/nestml/master/doc/tutorials/izhikevich/i…
I get the 'model' error; if I change model to neuron I get an extraneous input
'onRecieve' error. Are there any working models in nestml 7.0.2 that work?
-Chris
From: Babu, Pooja <p.babu@fz-juelich.de<mailto:p.babu@fz-juelich.de>>
Sent: 13 June 2024 10:40
To: NEST User Mailing List
<users@nest-simulator.org<mailto:users@nest-simulator.org>>
Subject: [NEST Users] Re: nestml syntax problem
You don't often get email from
p.babu@fz-juelich.de<mailto:p.babu@fz-juelich.de>. Learn why this is
important<https://aka.ms/LearnAboutSenderIdentification>
Hello Chris,
The latest release of NESTML (v7.0.2) uses the "neuron" or "synapse"
at the beginning of the model definition. We have unified this in our latest changes to
the language where they are replaced by "model", however, this is not yet
released.
It looks like you have conflicting versions of NESTML installed. I would suggest you
uninstall all the old NESTML instances and install it again via pip.
The pip-installed version should have models that begin with either "neuron" or
"synapse". The corresponding grammar can be found here:
https://github.com/nest/nestml/tree/v7.0.2/pynestml/grammars
Apologies for the confusion. We are in the process of doing a pre-release of the new
language changes soon.
Hope this helps!
Best regards,
Pooja
On 13. Jun 2024, at 11:11, thanh-binh.to@online.de<mailto:thanh-binh.to@online.de>
wrote:
Personal I'd like to recommend you to use the newest version of Nestml and to adapt
your old neuron model to the new syntax.
For doing it you have to compare a nestml model of any neuron in the current nestml
version to the old one.
Normally you have to put a word "end" at the end of each segment in model
Hope that help
BR Binh
Gesendet mit der mobilen Mail App
Am 13.06.24 um 10:59 schrieb Chris Huyck
Von: "Chris Huyck" <C.Huyck@mdx.ac.uk<mailto:C.Huyck@mdx.ac.uk>>
Datum: 13. Juni 2024
An: "NEST User Mailing List"
<users@nest-simulator.org<mailto:users@nest-simulator.org>>
Cc:
Betreff: [NEST Users] nestml syntax problem
I was using an old version of nest (3.5) and nestml. Someone sent me a nestml model, and
that worked. I wanted to make my own model, but the tutorials had a different format. In
particular, it seems like the first line of code in the tutorials start with model, and
the old version started with neuron of synapse.
So, I thought it was time to upgrade, so installed nest 3.7, and pip-ed nestml. (I also
installed PyNN as that's the way I typically work.) When I imported generate_target
(through python 3.12), I got the typical PyGSL warning; I think that's because I'm
using python 3.12 not 3.11, and I don't think it matters in this case.
Then I ran the generate_target and I got an error mismatched input 'model'
expecting {newline, 'neuron', 'synapse}
I expect there's something like a yacc table that specifies the syntax, and somehow
I've got the old syntax.
I've tried it with several version of nestml 7.0.2, 7.0.0, 6.0.0 and 5.0.0. I think
5.0.0 had the old syntax. I've tried several models from the library, and the
Izhikevich tutorial.
Any thoughts about how to fix it?
-Chris
_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
19 Jul
19 Jul
10:11 a.m.
I isolated the problem in pyNN. If I did a setup (as I usually do to start a simulation)
it loses access to the models made by nestml. I asked the PyNN folks for support, and
they said the problem was that (import pynn.nest as sim) sim.setup calls nest.Reset, which
loses the access. The solution is to use nest.Install("modulename").
-Chris
From: Babu, Pooja <p.babu(a)fz-juelich.de>
Sent: 19 June 2024 12:29
To: NEST User Mailing List <users(a)nest-simulator.org>
Subject: [NEST Users] Re: nestml syntax problem
Hello Chris,
If you want to generate the neuron models which has the same name in NEST, you can use the
"suffix" option in the "generate_nest_target" function. This adds the
suffix to the model name during code generation.
For example:
generate_nest_target(input_path="test_model.nestml",
target_path="target",
logging_level="INFO",
suffix="_nestml")
nest.Install("nestmlmodule")
n = nest.Create("test_model_nestml")
We do not currently provide pyNN support for NESTML models. If you manage to run NESTML
models in pyNN, do let us know.
Regards,
Pooja
On 19. Jun 2024, at 10:58, Chris Huyck
<C.Huyck@mdx.ac.uk<mailto:C.Huyck@mdx.ac.uk>> wrote:
I seem to be having problems with pyNN accessing the new model. I should note that the
first problem is that all of the 7.0.2 nesml models are already in the standard nest. So,
it's not clear, which version one is using. So, I switched to the ignore_and_fire
model, but changed the name to ignore_and_spike. A simple change of file name and model
name was sufficient. I got that running in pyNest. (It's a really simple model to
work with.)
I can also get it running in pyNN, but I can't use the Setup. If I do, it changes
something and I no longer have access to ignore_and_spike model. I'm using pyNN
0.12.3.
-Chris
From: Chris Huyck
Sent: 13 June 2024 16:34
To: NEST User Mailing List
<users@nest-simulator.org<mailto:users@nest-simulator.org>>
Subject: RE: [NEST Users] Re: nestml syntax problem
This was a pretty straight forward solution. I used the hill_tononi.nestml file below,
and nestml ran and compiled. The nest.Install works, but I can't actually run the
model. I'll try to sort that out.
So, thanks!
-Chris
From: Babu, Pooja <p.babu@fz-juelich.de<mailto:p.babu@fz-juelich.de>>
Sent: 13 June 2024 11:15
To: NEST User Mailing List
<users@nest-simulator.org<mailto:users@nest-simulator.org>>
Subject: [NEST Users] Re: nestml syntax problem
Hi Chris,
The keywords "model", "OnCondition" and "OnReceieve" are all
the new changes to the NESTML language which is not yet released.
As I mentioned earlier, it looks like you have the NESTML 7.0.2 installed, but the model
files you are using are the new ones with the language updates. The
"hill_tonini" model corresponding to your version should be:
https://github.com/nest/nestml/blob/v7.0.2/models/neurons/hill_tononi.nestml
We will fix the documentation to point to the "release version" to avoid further
confusion.
Regards,
Pooja
On 13. Jun 2024, at 11:55, Chris Huyck
<C.Huyck@mdx.ac.uk<mailto:C.Huyck@mdx.ac.uk>> wrote:
Hello Pooja,
Firstly, thanks for the quick response.
I've taken the hill_tononi_neuron model from Models library - NESTML documentation
1.0.0
documentation<https://nestml.readthedocs.io/en/latest/models_library/index.html>,
and it gives me the an error mismatched input 'model' expecting {newline,
'neuron', 'synapse}. I change model to neuron in the .nestml file, and I get
an extraneous input 'onCondition' error. If I try with izhekivich_task.nestml
fromraw.githubusercontent.com/nest/nestml/master/doc/tutorials/izhikevich/i…
I get the 'model' error; if I change model to neuron I get an extraneous input
'onRecieve' error. Are there any working models in nestml 7.0.2 that work?
-Chris
From: Babu, Pooja <p.babu@fz-juelich.de<mailto:p.babu@fz-juelich.de>>
Sent: 13 June 2024 10:40
To: NEST User Mailing List
<users@nest-simulator.org<mailto:users@nest-simulator.org>>
Subject: [NEST Users] Re: nestml syntax problem
You don't often get email from
p.babu@fz-juelich.de<mailto:p.babu@fz-juelich.de>. Learn why this is
important<https://aka.ms/LearnAboutSenderIdentification>
Hello Chris,
The latest release of NESTML (v7.0.2) uses the "neuron" or "synapse"
at the beginning of the model definition. We have unified this in our latest changes to
the language where they are replaced by "model", however, this is not yet
released.
It looks like you have conflicting versions of NESTML installed. I would suggest you
uninstall all the old NESTML instances and install it again via pip.
The pip-installed version should have models that begin with either "neuron" or
"synapse". The corresponding grammar can be found here:
https://github.com/nest/nestml/tree/v7.0.2/pynestml/grammars
Apologies for the confusion. We are in the process of doing a pre-release of the new
language changes soon.
Hope this helps!
Best regards,
Pooja
On 13. Jun 2024, at 11:11, thanh-binh.to@online.de<mailto:thanh-binh.to@online.de>
wrote:
Personal I'd like to recommend you to use the newest version of Nestml and to adapt
your old neuron model to the new syntax.
For doing it you have to compare a nestml model of any neuron in the current nestml
version to the old one.
Normally you have to put a word "end" at the end of each segment in model
Hope that help
BR Binh
Gesendet mit der mobilen Mail App
Am 13.06.24 um 10:59 schrieb Chris Huyck
Von: "Chris Huyck" <C.Huyck@mdx.ac.uk<mailto:C.Huyck@mdx.ac.uk>>
Datum: 13. Juni 2024
An: "NEST User Mailing List"
<users@nest-simulator.org<mailto:users@nest-simulator.org>>
Cc:
Betreff: [NEST Users] nestml syntax problem
I was using an old version of nest (3.5) and nestml. Someone sent me a nestml model, and
that worked. I wanted to make my own model, but the tutorials had a different format. In
particular, it seems like the first line of code in the tutorials start with model, and
the old version started with neuron of synapse.
So, I thought it was time to upgrade, so installed nest 3.7, and pip-ed nestml. (I also
installed PyNN as that's the way I typically work.) When I imported generate_target
(through python 3.12), I got the typical PyGSL warning; I think that's because I'm
using python 3.12 not 3.11, and I don't think it matters in this case.
Then I ran the generate_target and I got an error mismatched input 'model'
expecting {newline, 'neuron', 'synapse}
I expect there's something like a yacc table that specifies the syntax, and somehow
I've got the old syntax.
I've tried it with several version of nestml 7.0.2, 7.0.0, 6.0.0 and 5.0.0. I think
5.0.0 had the old syntax. I've tried several models from the library, and the
Izhikevich tutorial.
Any thoughts about how to fix it?
-Chris
_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
_______________________________________________
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users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
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155
days inactive
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days old
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Babu, Pooja -
Chris Huyck -
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