Hi Pooja, Thanks for the response. I have upgraded NESTML and now the error seems to be from new syntax. I changed my nestml file to say "model" instead of "synapse" and I changed to "emit_spike" (instead of "deliver_spike"). However, this is producing an error. I have attached both the updated nestml file and the error as printed to terminal.

Thanks!

On Wed, Jan 15, 2025 at 3:42 PM Babu, Pooja p.babu@fz-juelich.de wrote:

Hi Beck,

Thanks for writing in. From the errors, it looks like you might be using an older version of NESTML. We recently released version 8.0.0: https://github.com/nest/nestml/releases/tag/v8.0.0

Could you please update to the new version and try again? You could do that with the command “pip install nestml —upgrade”

Please let us know how you fare.

Regards, Pooja

On 15. Jan 2025, at 12:31, Beck Strohmer bstrohmer@gmail.com wrote:

Hi, I am trying to create a dopamine modulated synapse using NESTML. You can find the nestml file and the file for creating the neuron attached. I am using NEST version 3.8.0 and running within a conda environment (v. 24.1.2).

I get a make error in the end so the files are created except for the .so file that I need for loading the model. I attached the terminal error for further details. Has anyone else had this issue? How were you able to resolve it?

Thanks for any advice!

Best, Beck <compile_error.txt><dopamine_synapse_NEW.nestml> <create_gap_dopamod_synapse.py> _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

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Hi Pooja, This helped indeed! I was able to successfully make the new module. However, for some reason when I run my NEST simulation, it does not find this new neuron model. I have used the neuron model name which is defined by the C++ file. Additionally, the module successfully loads (this can be seen in the terminal output), but then it does not find the corresponding neuron model. You can find my installation terminal output attached and the terminal error when I try to load this neuron model.

Thanks again for your help!

On Thu, Jan 16, 2025 at 10:52 AM Babu, Pooja p.babu@fz-juelich.de wrote:

Hi Beck,

Along with the changes you mentioned, a few more modifications are needed.

1. The spike in the output block now has parameters that should match the

parameters in the emit_spike() function: https://nestml.readthedocs.io/en/latest/nestml_language/nestml_language_conc... In your case, it would be: output: spike(weight real, delay ms)

2. The integrate_odes() function should be called from the synapse. So a

corresponding update block should be added in the synapse: update: integrate_odes()

3. The decorator @nest::delay is no longer required. However, the delay

parameter and the weight must be provided to the generate_target() function via the codegen_opts: https://nestml.readthedocs.io/en/latest/running/running_nest.html#dendritic-...

codegen_opts={"neuron_synapse_pairs": [{"neuron": “<neuron_model>", "synapse": "dopamine_synapse", "vt_ports": ["dopa_spikes"]}], "delay_variable": {"dopamine_synapse": "d"}, "weight_variable": {"dopamine_synapse": "w"}})

Hope this helps!

Regards, Pooja

On 15. Jan 2025, at 18:19, Beck Strohmer bstrohmer@gmail.com wrote:

Hi Pooja, Thanks for the response. I have upgraded NESTML and now the error seems to be from new syntax. I changed my nestml file to say "model" instead of "synapse" and I changed to "emit_spike" (instead of "deliver_spike"). However, this is producing an error. I have attached both the updated nestml file and the error as printed to terminal.

Thanks!

On Wed, Jan 15, 2025 at 3:42 PM Babu, Pooja p.babu@fz-juelich.de wrote:

...

Hi Beck,

Thanks for writing in. From the errors, it looks like you might be using an older version of NESTML. We recently released version 8.0.0: https://github.com/nest/nestml/releases/tag/v8.0.0

Could you please update to the new version and try again? You could do that with the command “pip install nestml —upgrade”

Please let us know how you fare.

Regards, Pooja

On 15. Jan 2025, at 12:31, Beck Strohmer bstrohmer@gmail.com wrote:

Hi, I am trying to create a dopamine modulated synapse using NESTML. You can find the nestml file and the file for creating the neuron attached. I am using NEST version 3.8.0 and running within a conda environment (v. 24.1.2).

I get a make error in the end so the files are created except for the .so file that I need for loading the model. I attached the terminal error for further details. Has anyone else had this issue? How were you able to resolve it?

Thanks for any advice!

Best, Beck <compile_error.txt><dopamine_synapse_NEW.nestml> <create_gap_dopamod_synapse.py> _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

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<terminal_compile_error.txt><dopamine_synapse_NEW.nestml> _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

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This was the culprit, thanks so much for your help! My simulation is up and running. :)

On Thu, Jan 16, 2025 at 10:17 PM Babu, Pooja p.babu@fz-juelich.de wrote:

Hello Beck,

Please note that after NEST 3.7, the nest.Install() must be called after the nest.ResetKernel() because the latter unloads all the dynamically loaded modules. Please see: https://github.com/nest/nest-simulator/pull/3103

Could you check if these two calls are in the right order in your simulation script?

Regards, Pooja

On 16. Jan 2025, at 15:36, Beck Strohmer bstrohmer@gmail.com wrote:

Hi Pooja, This helped indeed! I was able to successfully make the new module. However, for some reason when I run my NEST simulation, it does not find this new neuron model. I have used the neuron model name which is defined by the C++ file. Additionally, the module successfully loads (this can be seen in the terminal output), but then it does not find the corresponding neuron model. You can find my installation terminal output attached and the terminal error when I try to load this neuron model.

Thanks again for your help!

On Thu, Jan 16, 2025 at 10:52 AM Babu, Pooja p.babu@fz-juelich.de wrote:

...

Hi Beck,

Along with the changes you mentioned, a few more modifications are needed.

1. The spike in the output block now has parameters that should match the

parameters in the emit_spike() function: https://nestml.readthedocs.io/en/latest/nestml_language/nestml_language_conc... In your case, it would be: output: spike(weight real, delay ms)

2. The integrate_odes() function should be called from the synapse. So a

corresponding update block should be added in the synapse: update: integrate_odes()

3. The decorator @nest::delay is no longer required. However, the delay

parameter and the weight must be provided to the generate_target() function via the codegen_opts: https://nestml.readthedocs.io/en/latest/running/running_nest.html#dendritic-...

codegen_opts={"neuron_synapse_pairs": [{"neuron": “<neuron_model>", "synapse": "dopamine_synapse", "vt_ports": ["dopa_spikes"]}], "delay_variable": {"dopamine_synapse": "d"}, "weight_variable": {"dopamine_synapse": "w"}})

Hope this helps!

Regards, Pooja

On 15. Jan 2025, at 18:19, Beck Strohmer bstrohmer@gmail.com wrote:

Hi Pooja, Thanks for the response. I have upgraded NESTML and now the error seems to be from new syntax. I changed my nestml file to say "model" instead of "synapse" and I changed to "emit_spike" (instead of "deliver_spike"). However, this is producing an error. I have attached both the updated nestml file and the error as printed to terminal.

Thanks!

On Wed, Jan 15, 2025 at 3:42 PM Babu, Pooja p.babu@fz-juelich.de wrote:

...

Hi Beck,

Thanks for writing in. From the errors, it looks like you might be using an older version of NESTML. We recently released version 8.0.0: https://github.com/nest/nestml/releases/tag/v8.0.0

Could you please update to the new version and try again? You could do that with the command “pip install nestml —upgrade”

Please let us know how you fare.

Regards, Pooja

On 15. Jan 2025, at 12:31, Beck Strohmer bstrohmer@gmail.com wrote:

Hi, I am trying to create a dopamine modulated synapse using NESTML. You can find the nestml file and the file for creating the neuron attached. I am using NEST version 3.8.0 and running within a conda environment (v. 24.1.2).

I get a make error in the end so the files are created except for the .so file that I need for loading the model. I attached the terminal error for further details. Has anyone else had this issue? How were you able to resolve it?

Thanks for any advice!

Best, Beck <compile_error.txt><dopamine_synapse_NEW.nestml> <create_gap_dopamod_synapse.py> _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

---

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<terminal_compile_error.txt><dopamine_synapse_NEW.nestml> _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

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<terminal_successful_installation.txt><terminal_not_found_error.txt> _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

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