Hello Thanh Binh To,

From the list of target files you have shared, the module name for the generated code is “nestmlmodule”. So in your simulation script, you must install “nestmlmodule” and not “iaf_psc_exp_nonlineardendrite”.

nest.Install(“nestmlmodule”) nest.Create(“iaf_psc_exp_nonlineardendrite”)

You do not need to copy the .so file manually as the generate_target() call already copies it to your install_path. Hope this helps!

Regards, Pooja

On 3. Jun 2024, at 13:22, Thanh Binh To thanh-binh.to@online.de wrote:

Dear all,

thanks you for very nice meeting today.

I use the following Python script for generating and compiling my NESTML-neuron model. It runs and provides the following files in my target order (see my snapshot) ######################### iaf_psc_exp_nonlineardendrite.h iaf_psc_exp_nonlineardendrite.cpp nestmlmodule.h nestmlmodule.cpp nestmlmodule.so #########################

##### my python script import sys from pathlib import Path from pynestml.frontend.pynestml_frontend import generate_target generate_target(input_path="/home/binh/experiments/nest-simulator-stdsp_synapse/iaf_psc_exp_nonlineardendrite.nestml", target_platform="NEST", install_path="/home/binh/experiments/nest-simulator-stdsp_synapse/models/") nest.Install("iaf_psc_exp_nonlineardendrite") ####

But I really do not know

1. where to copy nestmlmodule.so to?
2. What to do with generated C++ and *.h files? Copy to to the folder "models"??

Then I run other Python script to create a neuron (see my modified verion structural_plasticityB.py), and have got errors like ################################## File "/home/binh/experiments/nest-simulator/pynest/examples/structural_plasticityB.py", line 342, in <module> example.create_nodes() File "home/binh/experiments/nest-simulator/pynest/examples/structural_plasticityB.py", line 235, in create_nodes self.nodes_e = nest.Create('iaf_psc_exp_nonlineardendrite', ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/binh/experiments/nest-simulator/build/lib/python3.11/site-packages/nest/ll_api.py", line 228, in stack_checker_func return f(*args, **kwargs) ^^^^^^^^^^^^^^^^^^ File "/home/binh/experiments/nest-simulator/build/lib/python3.11/site-packages/nest/lib/hl_api_nodes.py", line 126, in Create sr(cmd) File "/home/binh/experiments/nest-simulator/build/lib/python3.11/site-packages/nest/ll_api.py", line 114, in catching_sli_run raise exceptionCls(commandname, message) nest.lib.hl_api_exceptions.NESTErrors.UnknownModelName: UnknownModelName in SLI function Create_l_i: /iaf_psc_exp_nonlineardendrite is not a known model name. Please check the modeldict for a list of available models. A frequent cause for this error is that NEST was compiled without the GNU Scientific Library, which is required for the conductance-based neuron models. ###################################

Can anyone help me?

Thanks With kind regards Mit freundlichen Grüßen

Thanh Binh To

Gesendet: Montag, 03. Juni 2024 um 10:32 Uhr Von: "Dennis Terhorst" d.terhorst@fz-juelich.de An: users@nest-simulator.org Betreff: [NEST Users] Open NEST Developer Video Conference Monday June 3, at 11:30 CEST (UTC+0200) Dear NEST Users & Developers!

I would like to invite you to our next fortnightly Open NEST Developer Video Conference today

Monday June 3, at 11:30 CEST (UTC+0200).

Despite many people attending conferences this week, we will briefly meet to offer attention also to smaller questions or more general topics that you may bring. The Project team round, might however be quite short today.

Feel free to join the meeting and bring your own quick questions for direct discussion or just to hear what's going on in and around NEST.

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/2024-06-03-Open-NEST-Developer-V...

Looking forward to seeing you soon!

Cheers,

Dennis Terhorst

Log-in information

We use a virtual conference room provided by DFN https://www.dfn.de/en/ (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 mailto: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

-- Dipl.-Phys. Dennis Terhorst Coordinator Software Development

Institute for Advanced Simulation (IAS-6), Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Institute of Neuroscience and Medicine

Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany

http://www.csn.fz-juelich.de/ Phone +49 2461 61-85062

---

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. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens

---

_______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org <iaf_psc_exp_nonlineardendrite.nestml><Screenshot from 2024-06-03 13-03-03.png><structural_plasticityB.py>_______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

Hello Thanh Binh To,

I see that the NESTML version you are using is quite old. Could you please install the latest version (7.0.2) and try again? You can install that using the command “pip install nestml”.

Please note that the module name should end with the suffix “module”. Therefore, your module name should be “iaf_psc_exp_nonlineardendrite_module” with an “e” at the end.

Regards, Pooja

On 7. Jun 2024, at 10:17, Thanh Binh To thanh-binh.to@online.de wrote:

Dear Pooja,

Yes I change the name of NEST-module to "iaf_psc_exp_nonlineardendrite_modul" ############### generate_target(input_path="/home/binh/experiments/Bouhadjar_SequenceDetection/nest-simulator-stdsp_synapse/build/Binh/iaf_psc_exp_nonlineardendrite.nestml", target_platform="NEST", module_name="iaf_psc_exp_nonlineardendrite_modul", install_path="/home/binh/experiments/Bouhadjar_SequenceDetection/nest-simulator-stdsp_synapse/models/") nest.Install("~/experiments/Bouhadjar_SequenceDetection/Bouhadjar_et_al_2021-1.0/module/iaf_psc_exp_nonlineardendrite_modul") ################

But have got errors ################ from pynestml.frontend.pynestml_frontend import generate_target File "/home/binh/.local/lib/python3.11/site-packages/NESTML-4.0.post0.dev0-py3.11.egg/pynestml/frontend/pynestml_frontend.py", line 39, in <module> from pynestml.utils.model_parser import ModelParser File "/home/binh/.local/lib/python3.11/site-packages/NESTML-4.0.post0.dev0-py3.11.egg/pynestml/utils/model_parser.py", line 28, in <module> from pynestml.generated.PyNestMLLexer import PyNestMLLexer File "/home/binh/.local/lib/python3.11/site-packages/NESTML-4.0.post0.dev0-py3.11.egg/pynestml/generated/PyNestMLLexer.py", line 314, in <module> class PyNestMLLexer(Lexer): File "/home/binh/.local/lib/python3.11/site-packages/NESTML-4.0.post0.dev0-py3.11.egg/pynestml/generated/PyNestMLLexer.py", line 316, in PyNestMLLexer atn = ATNDeserializer().deserialize(serializedATN()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/binh/programs/anaconda3/lib/python3.11/site-packages/antlr4/atn/ATNDeserializer.py", line 28, in deserialize self.checkVersion() File "/home/binh/programs/anaconda3/lib/python3.11/site-packages/antlr4/atn/ATNDeserializer.py", line 50, in checkVersion raise Exception("Could not deserialize ATN with version " + str(version) + " (expected " + str(SERIALIZED_VERSION) + ").") Exception: Could not deserialize ATN with version (expected 4). ####################

I do not know which ATN version should work ...

Thanks and BR Binh

Gesendet: Montag, 03. Juni 2024 um 16:54 Uhr Von: "Babu, Pooja" p.babu@fz-juelich.de An: "NEST User Mailing List" users@nest-simulator.org Betreff: [NEST Users] Re: Problem by generating my nestml Hello Thanh Binh To,

From the list of target files you have shared, the module name for the generated code is “nestmlmodule”. So in your simulation script, you must install “nestmlmodule” and not “iaf_psc_exp_nonlineardendrite”.

nest.Install(“nestmlmodule”) nest.Create(“iaf_psc_exp_nonlineardendrite”)

You do not need to copy the .so file manually as the generate_target() call already copies it to your install_path. Hope this helps!

Regards, Pooja

On 3. Jun 2024, at 13:22, Thanh Binh To thanh-binh.to@online.de wrote:

Dear all,

thanks you for very nice meeting today.

I use the following Python script for generating and compiling my NESTML-neuron model. It runs and provides the following files in my target order (see my snapshot) ######################### iaf_psc_exp_nonlineardendrite.h iaf_psc_exp_nonlineardendrite.cpp nestmlmodule.h nestmlmodule.cpp nestmlmodule.so #########################

##### my python script import sys from pathlib import Path from pynestml.frontend.pynestml_frontend import generate_target generate_target(input_path="/home/binh/experiments/nest-simulator-stdsp_synapse/iaf_psc_exp_nonlineardendrite.nestml", target_platform="NEST", install_path="/home/binh/experiments/nest-simulator-stdsp_synapse/models/") nest.Install("iaf_psc_exp_nonlineardendrite") ####

But I really do not know

1. where to copy nestmlmodule.so to?
2. What to do with generated C++ and *.h files? Copy to to the folder "models"??

Then I run other Python script to create a neuron (see my modified verion structural_plasticityB.py), and have got errors like ################################## File "/home/binh/experiments/nest-simulator/pynest/examples/structural_plasticityB.py", line 342, in <module> example.create_nodes() File "home/binh/experiments/nest-simulator/pynest/examples/structural_plasticityB.py", line 235, in create_nodes self.nodes_e = nest.Create('iaf_psc_exp_nonlineardendrite', ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/binh/experiments/nest-simulator/build/lib/python3.11/site-packages/nest/ll_api.py", line 228, in stack_checker_func return f(*args, **kwargs) ^^^^^^^^^^^^^^^^^^ File "/home/binh/experiments/nest-simulator/build/lib/python3.11/site-packages/nest/lib/hl_api_nodes.py", line 126, in Create sr(cmd) File "/home/binh/experiments/nest-simulator/build/lib/python3.11/site-packages/nest/ll_api.py", line 114, in catching_sli_run raise exceptionCls(commandname, message) nest.lib.hl_api_exceptions.NESTErrors.UnknownModelName: UnknownModelName in SLI function Create_l_i: /iaf_psc_exp_nonlineardendrite is not a known model name. Please check the modeldict for a list of available models. A frequent cause for this error is that NEST was compiled without the GNU Scientific Library, which is required for the conductance-based neuron models. ###################################

Can anyone help me?

Thanks With kind regards Mit freundlichen Grüßen

Thanh Binh To

Gesendet: Montag, 03. Juni 2024 um 10:32 Uhr Von: "Dennis Terhorst" d.terhorst@fz-juelich.de An: users@nest-simulator.org Betreff: [NEST Users] Open NEST Developer Video Conference Monday June 3, at 11:30 CEST (UTC+0200) Dear NEST Users & Developers!

I would like to invite you to our next fortnightly Open NEST Developer Video Conference today

Monday June 3, at 11:30 CEST (UTC+0200).

Despite many people attending conferences this week, we will briefly meet to offer attention also to smaller questions or more general topics that you may bring. The Project team round, might however be quite short today.

Feel free to join the meeting and bring your own quick questions for direct discussion or just to hear what's going on in and around NEST.

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/2024-06-03-Open-NEST-Developer-V...

Looking forward to seeing you soon!

Cheers,

Dennis Terhorst

Log-in information

We use a virtual conference room provided by DFN https://www.dfn.de/en/ (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 mailto: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

-- Dipl.-Phys. Dennis Terhorst Coordinator Software Development

Institute for Advanced Simulation (IAS-6), Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Institute of Neuroscience and Medicine

Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany

http://www.csn.fz-juelich.de/ Phone +49 2461 61-85062

---

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. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens

---

_______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org <iaf_psc_exp_nonlineardendrite.nestml><Screenshot from 2024-06-03 13-03-03.png><structural_plasticityB.py>_______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org