Hello everyone,
just a quick question in case anybody knows: is there a LIF model that has an adaptive spike threshold in NEST?
I know there's the GLIF model which can have a threshold, but it seems to bring other deviations from the conventional LIF model that I want to avoid. There's also the adaptive exponential integrate and fire model, but again I don't want the exponential part.
It's not a problem if no such model exists in NEST, I am only asking so I don't reimplement an existing model.
Any feedback would be appreciated.
Kind regards, Jona
Hi Jona,
Thanks for writing in! Could the NESTML model(s) used in the tutorial at https://nestml.readthedocs.io/en/latest/tutorials/spike_frequency_adaptation... be what you're looking for? In general, it's easy to take a NESTML model (see https://nestml.readthedocs.io/en/latest/models_library/index.html) and add a threshold adaptation mechanism to it. Please let us know how you fare! (Please make sure you're using the latest NESTML, v8.0.0-rc1 or the GitHub master version.)
With kind regards, Charl
On Tue, Sep 10, 2024, at 08:09, jona.m.scholz@gmail.com wrote:
Hello everyone,
just a quick question in case anybody knows: is there a LIF model that has an adaptive spike threshold in NEST?
I know there's the GLIF model which can have a threshold, but it seems to bring other deviations from the conventional LIF model that I want to avoid. There's also the adaptive exponential integrate and fire model, but again I don't want the exponential part.
It's not a problem if no such model exists in NEST, I am only asking so I don't reimplement an existing model.
Any feedback would be appreciated.
Kind regards, Jona _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
Hi Jona,
you might also be interested in the leaky integrate-and-fire model with adaptive threshold [https://nest-simulator.readthedocs.io/en/latest/models/mat2_psc_exp.html]. Here, the voltage is not reset after a threshold crossing, though.
Best
Anno
On 10.09.24 09:15, Charl Linssen wrote:
Hi Jona,
Thanks for writing in! Could the NESTML model(s) used in the tutorial at https://nestml.readthedocs.io/en/latest/tutorials/spike_frequency_adaptation... be what you're looking for? In general, it's easy to take a NESTML model (see https://nestml.readthedocs.io/en/latest/models_library/index.html) and add a threshold adaptation mechanism to it. Please let us know how you fare! (Please make sure you're using the latest NESTML, v8.0.0-rc1 or the GitHub master version.)
With kind regards, Charl
On Tue, Sep 10, 2024, at 08:09, jona.m.scholz@gmail.com wrote:
Hello everyone,
just a quick question in case anybody knows: is there a LIF model that has an adaptive spike threshold in NEST?
I know there's the GLIF model which can have a threshold, but it seems to bring other deviations from the conventional LIF model that I want to avoid. There's also the adaptive exponential integrate and fire model, but again I don't want the exponential part.
It's not a problem if no such model exists in NEST, I am only asking so I don't reimplement an existing model.
Any feedback would be appreciated.
Kind regards, Jona _______________________________________________ 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
Dear Charl and Anno,
Thank you for your replies.
I hadn't heard about neurons that don't reset and will have to look into it more. Thank you :)
I can't seem to run the SFA neuron tutorial linked in Charl's reply. It fails in the first call to NESTCodeGeneratorUtils.generate_code_for(...) with an error found below. I have tried it on two Ubuntu systems using NestML versions 8.0.0-rc1 and 8.0.0-rc2 with the iaf_psc_alpha_neuron.nestml model from the NestML master branch. It is probably just some technical problem on my end and I'm sure I will be able to resolve it soon. Nonetheless, if anyone spots something obvious in the error message below, please let me know.
Thanks for your help and have a great day!
Kind regards, Jona
The error message: --------------------------------------------------------------------------- CalledProcessError Traceback (most recent call last) File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:174, in NESTBuilder.build(self) 173 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:173 current_stage = "build" --> 174 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:174 subprocess.check_call(make_all_cmd, stderr=stderr, stdout=stdout, shell=shell, 175 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:175 cwd=str(os.path.join(target_path))) 176 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:176 current_stage = "install" File ~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:369, in check_call(*popenargs, **kwargs) 368 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:368 cmd = popenargs[0] --> 369 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:369 raise CalledProcessError(retcode, cmd) 370 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:370 return 0 CalledProcessError: Command '['make', '-j8', 'all']' returned non-zero exit status 2. During handling of the above exception, another exception occurred: GeneratedCodeBuildException Traceback (most recent call last) Cell In[2], line 3 1 # generate and build code 2 module_name_no_sfa, neuron_model_name_no_sfa = \ ----> 3 NESTCodeGeneratorUtils. generate_code_for("iaf_psc_alpha_neuron.nestml") File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:136, in NESTCodeGeneratorUtils.generate_code_for(cls, nestml_neuron_model, nestml_synapse_model, module_name, target_path, post_ports, mod_ports, codegen_opts, logging_level) 133 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:133 uniq_id = str(uuid.uuid4().hex) 134 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:134 module_name = "nestml_" + uniq_id + "_module" --> 136 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:136 generate_nest_target(input_path=input_fns, 137 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:137 install_path=install_path, 138 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:138 logging_level=logging_level, 139 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:139 module_name=module_name, 140 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:140 target_path=target_path, 141 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:141 suffix="_nestml", 142 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:142 codegen_opts=_codegen_opts) 144 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:144 if nestml_synapse_model: 145 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:145 return module_name, mangled_neuron_name, mangled_synapse_name File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:270, in generate_nest_target(input_path, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts) 243 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:243 def generate_nest_target(input_path: Union[str, Sequence[str]], target_path: Optional[str] = None, 244 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:244 install_path: Optional[str] = None, logging_level="ERROR", 245 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:245 module_name=None, store_log: bool = False, suffix: str = "", 246 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:246 dev: bool = False, codegen_opts: Optional[Mapping[str, Any]] = None): 247 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:247 r"""Generate and build code for NEST Simulator. 248 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:248 249 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:249 Parameters (...) 268 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:268 A dictionary containing additional options for the target code generator. 269 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:269 """ --> 270 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:270 generate_target(input_path, target_platform="NEST", target_path=target_path, logging_level=logging_level, 271 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:271 module_name=module_name, store_log=store_log, suffix=suffix, install_path=install_path, 272 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:272 dev=dev, codegen_opts=codegen_opts) File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:193, in generate_target(input_path, target_platform, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts) 165 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:165 r"""Generate and build code for the given target platform. 166 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:166 167 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:167 Parameters (...) 188 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:188 A dictionary containing additional options for the target code generator. 189 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:189 """ 191 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:191 configure_front_end(input_path, target_platform, target_path, install_path, logging_level, 192 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:192 module_name, store_log, suffix, dev, codegen_opts) --> 193 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:193 if not process() == 0: 194 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:194 raise Exception("Error(s) occurred while processing the model") File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:482, in process() 480 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:480 # perform build 481 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:481 if _builder is not None: --> 482 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:482 _builder.build() 484 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:484 if FrontendConfiguration.store_log: 485 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:485 store_log_to_file() File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:181, in NESTBuilder.build(self) 177 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:177 subprocess.check_call(make_install_cmd, stderr=stderr, stdout=stdout, shell=shell, 178 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:178 cwd=str(os.path.join(target_path))) 180 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:180 except subprocess.CalledProcessError as e: --> 181 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:181 raise GeneratedCodeBuildException(stages_exception[current_stage]) 183 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:183 finally: 184 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:184 if self._options["redirect"]:
On Tue, Sep 10, 2024 at 9:33 AM Anno Kurth a.kurth@fz-juelich.de wrote:
Hi Jona,
you might also be interested in the leaky integrate-and-fire model with adaptive threshold [https://nest-simulator.readthedocs.io/en/latest/models/mat2_psc_exp.html ]. Here, the voltage is not reset after a threshold crossing, though.
Best
Anno
On 10.09.24 09:15, Charl Linssen wrote:
Hi Jona,
Thanks for writing in! Could the NESTML model(s) used in the tutorial at
https://nestml.readthedocs.io/en/latest/tutorials/spike_frequency_adaptation... be what you're looking for? In general, it's easy to take a NESTML model (see https://nestml.readthedocs.io/en/latest/models_library/index.html) and add a threshold adaptation mechanism to it. Please let us know how you fare! (Please make sure you're using the latest NESTML, v8.0.0-rc1 or the GitHub master version.)
With kind regards, Charl
On Tue, Sep 10, 2024, at 08:09, jona.m.scholz@gmail.com wrote:
Hello everyone,
just a quick question in case anybody knows: is there a LIF model that has an adaptive spike threshold in NEST?
I know there's the GLIF model which can have a threshold, but it seems to bring other deviations from the conventional LIF model that I want to avoid. There's also the adaptive exponential integrate and fire model, but again I don't want the exponential part.
It's not a problem if no such model exists in NEST, I am only asking so I don't reimplement an existing model.
Any feedback would be appreciated.
Kind regards, Jona _______________________________________________ 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
-- Anno Kurth Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience Jülich Research Centre Jülich, Germany
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 Geschäftsführung: 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
Hi Jona,
Sorry about the error. It might be related to the conda environment; the issue seems to be that there is an error during compilation, but the error message is not shown in these logs. Could you check in your terminal (that you used to launch the Jupyter notebook server) for the error messages from gcc?
Cheers, Charl
On Wed, Sep 11, 2024, at 22:06, Jona Scholz wrote:
Dear Charl and Anno,
Thank you for your replies.
I hadn't heard about neurons that don't reset and will have to look into it more. Thank you :)
I can't seem to run the SFA neuron tutorial linked in Charl's reply. It fails in the first call to NESTCodeGeneratorUtils.generate_code_for(...) with an error found below. I have tried it on two Ubuntu systems using NestML versions 8.0.0-rc1 and 8.0.0-rc2 with the iaf_psc_alpha_neuron.nestml model from the NestML master branch. It is probably just some technical problem on my end and I'm sure I will be able to resolve it soon. Nonetheless, if anyone spots something obvious in the error message below, please let me know.
Thanks for your help and have a great day!
Kind regards, Jona
The error message: --------------------------------------------------------------------------- CalledProcessError Traceback (most recent call last) File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:174, in NESTBuilder.build(self) * 173 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:173 current_stage **=** **"**build**"** *--> 174 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:174 subprocess.check_call(make_all_cmd, stderr=stderr, stdout=stdout, shell=shell, * 175 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:175 cwd**=**str**(os**.**path**.**join(target_path))) ** 176 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:176 current_stage **=** **"**install**"** File *~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:369, in check_call(*popenargs, **kwargs) * 368 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:368 cmd **=** popenargs[**0**] *--> 369 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:369 raise CalledProcessError(retcode, cmd) * 370 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:370 **return* 0 CalledProcessError: Command '['make', '-j8', 'all']' returned non-zero exit status 2. During handling of the above exception, another exception occurred: GeneratedCodeBuildException Traceback (most recent call last) Cell In[2], line 3 * 1 **# generate and build code* * 2 module_name_no_sfa, neuron_model_name_no_sfa **=** \ *----> 3 NESTCodeGeneratorUtils.generate_code_for("iaf_psc_alpha_neuron.nestml") File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:136, in NESTCodeGeneratorUtils.generate_code_for(cls, nestml_neuron_model, nestml_synapse_model, module_name, target_path, post_ports, mod_ports, codegen_opts, logging_level) * 133 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:133 uniq_id **=** **str**(uuid**.**uuid4()**.**hex) ** 134 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:134 module_name **=** **"**nestml_**"** **+** uniq_id **+** **"**_module**"** *--> 136 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:136 generate_nest_target(input_path=input_fns, * 137 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:137 install_path**=**install_path, ** 138 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:138 logging_level**=**logging_level, ** 139 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:139 module_name**=**module_name, ** 140 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:140 target_path**=**target_path, ** 141 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:141 suffix**=**"**_nestml**"**, ** 142 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:142 codegen_opts**=**_codegen_opts) ** 144 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:144 **if* nestml_synapse_model: * 145 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:145 **return* module_name, mangled_neuron_name, mangled_synapse_name File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:270, in generate_nest_target(input_path, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts) * 243 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:243 **def* generate_nest_target(input_path: Union[str, Sequence[str]], target_path: Optional[str] = None, * 244 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:244 install_path: Optional[**str**] **=** **None*, logging_level="ERROR", * 245 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:245 module_name**=**None*, store_log: bool = False, suffix: str = "", * 246 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:246 dev: **bool** **=** **False*, codegen_opts: Optional[Mapping[str, Any]] = None): * 247 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:247 ** **r**"""Generate and build code for NEST Simulator.* * 248 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:248 ** 249 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:249 ** Parameters* (...) * 268 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:268 ** A dictionary containing additional options for the target code generator.* * 269 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:269 ** """* --> 270 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:270 generate_target(input_path, target_platform="NEST", target_path=target_path, logging_level=logging_level, * 271 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:271 module_name**=**module_name, store_log**=**store_log, suffix**=**suffix, install_path**=**install_path, ** 272 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:272 dev**=**dev, codegen_opts**=**codegen_opts) File *~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:193, in generate_target(input_path, target_platform, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts) * 165 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:165 **r**"""Generate and build code for the given target platform.* * 166 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:166 ** 167 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:167 **Parameters* (...) * 188 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:188 ** A dictionary containing additional options for the target code generator.* * 189 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:189 **"""* * 191 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:191 configure_front_end(input_path, target_platform, target_path, install_path, logging_level, ** 192 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:192 module_name, store_log, suffix, dev, codegen_opts) *--> 193 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:193 if not process() == 0: * 194 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:194 **raise* Exception("Error(s) occurred while processing the model") File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:482, in process() * 480 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:480 **# perform build* * 481 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:481 **if* _builder is not None: --> 482 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:482 _builder.build() * 484 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:484 **if* FrontendConfiguration.store_log: * 485 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:485 store_log_to_file() File *~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:181, in NESTBuilder.build(self) * 177 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:177 subprocess**.**check_call(make_install_cmd, stderr**=**stderr, stdout**=**stdout, shell**=**shell, ** 178 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:178 cwd**=**str**(os**.**path**.**join(target_path))) ** 180 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:180 **except* subprocess.CalledProcessError as e: --> 181 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:181 raise GeneratedCodeBuildException(stages_exception[current_stage]) * 183 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:183 **finally*: * 184 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:184 **if* self._options["redirect"]:
On Tue, Sep 10, 2024 at 9:33 AM Anno Kurth a.kurth@fz-juelich.de wrote:
Hi Jona,
you might also be interested in the leaky integrate-and-fire model with adaptive threshold [https://nest-simulator.readthedocs.io/en/latest/models/mat2_psc_exp.html]. Here, the voltage is not reset after a threshold crossing, though.
Best
Anno
On 10.09.24 09:15, Charl Linssen wrote:
Hi Jona,
Thanks for writing in! Could the NESTML model(s) used in the tutorial at https://nestml.readthedocs.io/en/latest/tutorials/spike_frequency_adaptation... be what you're looking for? In general, it's easy to take a NESTML model (see https://nestml.readthedocs.io/en/latest/models_library/index.html) and add a threshold adaptation mechanism to it. Please let us know how you fare! (Please make sure you're using the latest NESTML, v8.0.0-rc1 or the GitHub master version.)
With kind regards, Charl
On Tue, Sep 10, 2024, at 08:09, jona.m.scholz@gmail.com wrote:
Hello everyone,
just a quick question in case anybody knows: is there a LIF model that has an adaptive spike threshold in NEST?
I know there's the GLIF model which can have a threshold, but it seems to bring other deviations from the conventional LIF model that I want to avoid. There's also the adaptive exponential integrate and fire model, but again I don't want the exponential part.
It's not a problem if no such model exists in NEST, I am only asking so I don't reimplement an existing model.
Any feedback would be appreciated.
Kind regards, Jona _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
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-- Anno Kurth Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience Jülich Research Centre Jülich, Germany
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 Geschäftsführung: 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
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Hi Charl,
The terminal logs are shown below. Is that the error message you were looking for?
Thanks for your help :)
Kind regards, Jona
CMake Warning (dev) at CMakeLists.txt:93 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it.
-- The CXX compiler identification is GNU 11.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /home/jona/miniconda3/envs/neuro/bin/x86_64-conda-linux-gnu-c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done
------------------------------------------------------- nestml_7f8d1ff3e3e8497da87659816759e61b_module Configuration Summary -------------------------------------------------------
C++ compiler : /home/jona/miniconda3/envs/neuro/bin/x86_64-conda-linux-gnu-c++ Build static libs : OFF C++ compiler flags : -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jona/miniconda3/envs/neuro/include NEST compiler flags : -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jona/miniconda3/envs/neuro/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/nest-simulator_1724732927678/work=/usr/local/src/conda/nest-simulator-3.8 -fdebug-prefix-map=/home/jona/miniconda3/envs/neuro=/usr/local/src/conda-prefix -lrt -std=c++17 -Wall -fopenmp -O2 -fdiagnostics-color=auto NEST include dirs : -I/home/jona/miniconda3/envs/neuro/include/nest -I/home/jona/miniconda3/envs/neuro/include -I/home/jona/miniconda3/envs/neuro/include -I/home/jona/miniconda3/envs/neuro/include -I/home/jona/miniconda3/envs/neuro/include NEST libraries flags : -L/home/jona/miniconda3/envs/neuro/lib/nest -lnest -lsli /home/jona/miniconda3/envs/neuro/x86_64-conda-linux-gnu/sysroot/usr/lib/libpthread.so
-------------------------------------------------------
You can now build and install 'nestml_7f8d1ff3e3e8497da87659816759e61b_module' using make make install
The library file libnestml_7f8d1ff3e3e8497da87659816759e61b_module.so will be installed to /tmp/nestml_target_t1m_k1tx The module can be loaded into NEST using (nestml_7f8d1ff3e3e8497da87659816759e61b_module) Install (in SLI) nest.Install(nestml_7f8d1ff3e3e8497da87659816759e61b_module) (in PyNEST)
CMake Warning (dev) in CMakeLists.txt: No cmake_minimum_required command is present. A line of code such as
cmake_minimum_required(VERSION 3.30)
should be added at the top of the file. The version specified may be lower if you wish to support older CMake versions for this project. For more information run "cmake --help-policy CMP0000". This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring done (3.7s) -- Generating done (0.0s) -- Build files have been written to: /home/jona/rstdp-gym/target [ 66%] Building CXX object CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/iaf_psc_alpha_neuron_nestml.o [ 66%] Building CXX object CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/nestml_7f8d1ff3e3e8497da87659816759e61b_module.o In file included from /home/jona/miniconda3/envs/neuro/include/nest/sort.h:36, from /home/jona/miniconda3/envs/neuro/include/nest/connector_base.h:35, from /home/jona/miniconda3/envs/neuro/include/nest/connection_manager.h:36, from /home/jona/miniconda3/envs/neuro/include/nest/connection_manager_impl.h:26, from /home/jona/rstdp-gym/target/nestml_7f8d1ff3e3e8497da87659816759e61b_module.cpp:26: /home/jona/miniconda3/envs/neuro/include/nest/iterator_pair.h:26:10: fatal error: boost/iterator/iterator_adaptor.hpp: No such file or directory 26 | #include <boost/iterator/iterator_adaptor.hpp> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. In file included from /home/jona/miniconda3/envs/neuro/include/nest/sort.h:36, from /home/jona/miniconda3/envs/neuro/include/nest/connector_base.h:35, from /home/jona/miniconda3/envs/neuro/include/nest/connection_manager.h:36, from /home/jona/miniconda3/envs/neuro/include/nest/kernel_manager.h:30, from /home/jona/rstdp-gym/target/iaf_psc_alpha_neuron_nestml.cpp:33: /home/jona/miniconda3/envs/neuro/include/nest/iterator_pair.h:26:10: fatal error: boost/iterator/iterator_adaptor.hpp: No such file or directory 26 | #include <boost/iterator/iterator_adaptor.hpp> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[2]: *** [CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/build.make:76: CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/nestml_7f8d1ff3e3e8497da87659816759e61b_module.o] Error 1 make[2]: *** Waiting for unfinished jobs.... make[2]: *** [CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/build.make:90: CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/iaf_psc_alpha_neuron_nestml.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:110: CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/all] Error 2 make: *** [Makefile:156: all] Error 2
On Thu, Sep 12, 2024 at 12:17 PM Charl Linssen nest-users@turingbirds.com wrote:
Hi Jona,
Sorry about the error. It might be related to the conda environment; the issue seems to be that there is an error during compilation, but the error message is not shown in these logs. Could you check in your terminal (that you used to launch the Jupyter notebook server) for the error messages from gcc?
Cheers, Charl
On Wed, Sep 11, 2024, at 22:06, Jona Scholz wrote:
Dear Charl and Anno,
Thank you for your replies.
I hadn't heard about neurons that don't reset and will have to look into it more. Thank you :)
I can't seem to run the SFA neuron tutorial linked in Charl's reply. It fails in the first call to NESTCodeGeneratorUtils.generate_code_for(...) with an error found below. I have tried it on two Ubuntu systems using NestML versions 8.0.0-rc1 and 8.0.0-rc2 with the iaf_psc_alpha_neuron.nestml model from the NestML master branch. It is probably just some technical problem on my end and I'm sure I will be able to resolve it soon. Nonetheless, if anyone spots something obvious in the error message below, please let me know.
Thanks for your help and have a great day!
Kind regards, Jona
The error message:
CalledProcessError Traceback (most recent call last) File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:174, in NESTBuilder.build(self) * 173 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:173 current_stage **=* *"**build**"* --> 174 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:174 subprocess.check_call(make_all_cmd, stderr=stderr, stdout=stdout, shell=shell,
- 175
https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:175 cwd**=**str**(os**.**path**.**join(target_path))) ** 176 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:176 current_stage **=* *"**install**"** File * ~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:369, in check_call(*popenargs, **kwargs) * 368 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:368 cmd **=** popenargs[**0**] *--> 369 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:369 raise CalledProcessError(retcode, cmd) * 370 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:370 **return* 0 CalledProcessError: Command '['make', '-j8', 'all']' returned non-zero exit status 2. During handling of the above exception, another exception occurred: GeneratedCodeBuildException Traceback (most recent call last) Cell In[2], line 3 * 1 **# generate and build code* * 2 module_name_no_sfa, neuron_model_name_no_sfa **=** \ *----> 3 NESTCodeGeneratorUtils.generate_code_for("iaf_psc_alpha_neuron.nestml") File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:136, in NESTCodeGeneratorUtils.generate_code_for(cls, nestml_neuron_model, nestml_synapse_model, module_name, target_path, post_ports, mod_ports, codegen_opts, logging_level) * 133 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:133 uniq_id **=* *str**(uuid**.**uuid4()**.**hex) ** 134 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:134 module_name **=* *"**nestml_**"* *+** uniq_id **+* *"**_module**"* --> 136 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:136 generate_nest_target(input_path=input_fns, * 137 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:137 install_path**=**install_path, ** 138 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:138 logging_level**=**logging_level, ** 139 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:139 module_name**=**module_name, ** 140 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:140 target_path**=**target_path, ** 141 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:141 suffix**=**"**_nestml**"**, ** 142 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:142 codegen_opts**=**_codegen_opts) ** 144 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:144 **if* nestml_synapse_model: * 145 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:145 **return* module_name, mangled_neuron_name, mangled_synapse_name File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:270, in generate_nest_target(input_path, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts) * 243 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:243 **def* generate_nest_target(input_path: Union[str, Sequence[str]], target_path: Optional[str] = None, * 244 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:244 install_path: Optional[**str**] **=* *None*, logging_level="ERROR", * 245 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:245 module_name**=**None*, store_log: bool = False, suffix: str = "", * 246 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:246 dev: **bool* *=* *False*, codegen_opts: Optional[Mapping[str, Any]] = None):
- 247
- *r**"""Generate and build code for NEST Simulator.* * 248
https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:248 ** 249 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:249 ** Parameters* (...) * 268 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:268 ** A dictionary containing additional options for the target code generator.* * 269 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:269 ** """* --> 270 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:270 generate_target(input_path, target_platform="NEST", target_path=target_path, logging_level=logging_level, * 271 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:271 module_name**=**module_name, store_log**=**store_log, suffix**=**suffix, install_path**=**install_path, ** 272 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:272 dev**=**dev, codegen_opts**=**codegen_opts) File * ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:193, in generate_target(input_path, target_platform, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts) * 165 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:165 **r**"""Generate and build code for the given target platform.* * 166 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:166 ** 167 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:167 **Parameters* (...) * 188 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:188 ** A dictionary containing additional options for the target code generator.* * 189 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:189 **"""* * 191 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:191 configure_front_end(input_path, target_platform, target_path, install_path, logging_level, ** 192 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:192 module_name, store_log, suffix, dev, codegen_opts) *--> 193 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:193 if not process() == 0: * 194 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:194 **raise* Exception("Error(s) occurred while processing the model") File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:482, in process() * 480 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:480 **# perform build* * 481 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:481 **if* _builder is not None: --> 482 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:482 _builder.build() * 484 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:484 **if* FrontendConfiguration.store_log: * 485 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:485 store_log_to_file() File * ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:181, in NESTBuilder.build(self) * 177 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:177 subprocess**.**check_call(make_install_cmd, stderr**=**stderr, stdout**=**stdout, shell**=**shell, ** 178 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:178 cwd**=**str**(os**.**path**.**join(target_path))) ** 180 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:180 **except* subprocess.CalledProcessError as e: --> 181 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:181 raise GeneratedCodeBuildException(stages_exception[current_stage]) * 183 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:183 **finally*: * 184 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:184 **if* self._options["redirect"]:
On Tue, Sep 10, 2024 at 9:33 AM Anno Kurth a.kurth@fz-juelich.de wrote:
Hi Jona,
you might also be interested in the leaky integrate-and-fire model with adaptive threshold [https://nest-simulator.readthedocs.io/en/latest/models/mat2_psc_exp.html ]. Here, the voltage is not reset after a threshold crossing, though.
Best
Anno
On 10.09.24 09:15, Charl Linssen wrote:
Hi Jona,
Thanks for writing in! Could the NESTML model(s) used in the tutorial at
https://nestml.readthedocs.io/en/latest/tutorials/spike_frequency_adaptation... be what you're looking for? In general, it's easy to take a NESTML model (see https://nestml.readthedocs.io/en/latest/models_library/index.html) and add a threshold adaptation mechanism to it. Please let us know how you fare! (Please make sure you're using the latest NESTML, v8.0.0-rc1 or the GitHub master version.)
With kind regards, Charl
On Tue, Sep 10, 2024, at 08:09, jona.m.scholz@gmail.com wrote:
Hello everyone,
just a quick question in case anybody knows: is there a LIF model that has an adaptive spike threshold in NEST?
I know there's the GLIF model which can have a threshold, but it seems to bring other deviations from the conventional LIF model that I want to avoid. There's also the adaptive exponential integrate and fire model, but again I don't want the exponential part.
It's not a problem if no such model exists in NEST, I am only asking so I don't reimplement an existing model.
Any feedback would be appreciated.
Kind regards, Jona _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
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-- Anno Kurth Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience Jülich Research Centre Jülich, Germany
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 Geschäftsführung: 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
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Ah, yes, that is indeed very informative. It indicates that the Boost C++ libraries are missing. Would it be possible for you to add Boost to the conda environment?
Perhaps you could check the full installation instructions for NESTML on Anaconda at: https://nestml.readthedocs.io/en/latest/installation.html#anaconda-installat...
Hope this helps! Charl
On Fri, Sep 13, 2024, at 09:41, Jona Scholz wrote:
Hi Charl,
The terminal logs are shown below. Is that the error message you were looking for?
Thanks for your help :)
Kind regards, Jona
CMake Warning (dev) at CMakeLists.txt:93 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it.
-- The CXX compiler identification is GNU 11.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /home/jona/miniconda3/envs/neuro/bin/x86_64-conda-linux-gnu-c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done
nestml_7f8d1ff3e3e8497da87659816759e61b_module Configuration Summary
C++ compiler : /home/jona/miniconda3/envs/neuro/bin/x86_64-conda-linux-gnu-c++ Build static libs : OFF C++ compiler flags : -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jona/miniconda3/envs/neuro/include NEST compiler flags : -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jona/miniconda3/envs/neuro/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/nest-simulator_1724732927678/work=/usr/local/src/conda/nest-simulator-3.8 -fdebug-prefix-map=/home/jona/miniconda3/envs/neuro=/usr/local/src/conda-prefix -lrt -std=c++17 -Wall -fopenmp -O2 -fdiagnostics-color=auto NEST include dirs : -I/home/jona/miniconda3/envs/neuro/include/nest -I/home/jona/miniconda3/envs/neuro/include -I/home/jona/miniconda3/envs/neuro/include -I/home/jona/miniconda3/envs/neuro/include -I/home/jona/miniconda3/envs/neuro/include NEST libraries flags : -L/home/jona/miniconda3/envs/neuro/lib/nest -lnest -lsli /home/jona/miniconda3/envs/neuro/x86_64-conda-linux-gnu/sysroot/usr/lib/libpthread.so
You can now build and install 'nestml_7f8d1ff3e3e8497da87659816759e61b_module' using make make install
The library file libnestml_7f8d1ff3e3e8497da87659816759e61b_module.so will be installed to /tmp/nestml_target_t1m_k1tx The module can be loaded into NEST using (nestml_7f8d1ff3e3e8497da87659816759e61b_module) Install (in SLI) nest.Install(nestml_7f8d1ff3e3e8497da87659816759e61b_module) (in PyNEST)
CMake Warning (dev) in CMakeLists.txt: No cmake_minimum_required command is present. A line of code such as
cmake_minimum_required(VERSION 3.30)should be added at the top of the file. The version specified may be lower if you wish to support older CMake versions for this project. For more information run "cmake --help-policy CMP0000". This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring done (3.7s) -- Generating done (0.0s) -- Build files have been written to: /home/jona/rstdp-gym/target [ 66%] Building CXX object CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/iaf_psc_alpha_neuron_nestml.o [ 66%] Building CXX object CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/nestml_7f8d1ff3e3e8497da87659816759e61b_module.o In file included from /home/jona/miniconda3/envs/neuro/include/nest/sort.h:36, from /home/jona/miniconda3/envs/neuro/include/nest/connector_base.h:35, from /home/jona/miniconda3/envs/neuro/include/nest/connection_manager.h:36, from /home/jona/miniconda3/envs/neuro/include/nest/connection_manager_impl.h:26, from /home/jona/rstdp-gym/target/nestml_7f8d1ff3e3e8497da87659816759e61b_module.cpp:26: /home/jona/miniconda3/envs/neuro/include/nest/iterator_pair.h:26:10: fatal error: boost/iterator/iterator_adaptor.hpp: No such file or directory 26 | #include <boost/iterator/iterator_adaptor.hpp> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. In file included from /home/jona/miniconda3/envs/neuro/include/nest/sort.h:36, from /home/jona/miniconda3/envs/neuro/include/nest/connector_base.h:35, from /home/jona/miniconda3/envs/neuro/include/nest/connection_manager.h:36, from /home/jona/miniconda3/envs/neuro/include/nest/kernel_manager.h:30, from /home/jona/rstdp-gym/target/iaf_psc_alpha_neuron_nestml.cpp:33: /home/jona/miniconda3/envs/neuro/include/nest/iterator_pair.h:26:10: fatal error: boost/iterator/iterator_adaptor.hpp: No such file or directory 26 | #include <boost/iterator/iterator_adaptor.hpp> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[2]: *** [CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/build.make:76: CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/nestml_7f8d1ff3e3e8497da87659816759e61b_module.o] Error 1 make[2]: *** Waiting for unfinished jobs.... make[2]: *** [CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/build.make:90: CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/iaf_psc_alpha_neuron_nestml.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:110: CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/all] Error 2 make: *** [Makefile:156: all] Error 2
On Thu, Sep 12, 2024 at 12:17 PM Charl Linssen nest-users@turingbirds.com wrote:
__ Hi Jona,
Sorry about the error. It might be related to the conda environment; the issue seems to be that there is an error during compilation, but the error message is not shown in these logs. Could you check in your terminal (that you used to launch the Jupyter notebook server) for the error messages from gcc?
Cheers, Charl
On Wed, Sep 11, 2024, at 22:06, Jona Scholz wrote:
Dear Charl and Anno,
Thank you for your replies.
I hadn't heard about neurons that don't reset and will have to look into it more. Thank you :)
I can't seem to run the SFA neuron tutorial linked in Charl's reply. It fails in the first call to NESTCodeGeneratorUtils.generate_code_for(...) with an error found below. I have tried it on two Ubuntu systems using NestML versions 8.0.0-rc1 and 8.0.0-rc2 with the iaf_psc_alpha_neuron.nestml model from the NestML master branch. It is probably just some technical problem on my end and I'm sure I will be able to resolve it soon. Nonetheless, if anyone spots something obvious in the error message below, please let me know.
Thanks for your help and have a great day!
Kind regards, Jona
The error message: --------------------------------------------------------------------------- CalledProcessError Traceback (most recent call last) File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:174, in NESTBuilder.build(self) * 173 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:173 current_stage **=** **"**build**"** *--> 174 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:174 subprocess.check_call(make_all_cmd, stderr=stderr, stdout=stdout, shell=shell, * 175 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:175 cwd**=**str**(os**.**path**.**join(target_path))) ** 176 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:176 current_stage **=** **"**install**"** File *~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:369, in check_call(*popenargs, **kwargs) * 368 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:368 cmd **=** popenargs[**0**] *--> 369 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:369 raise CalledProcessError(retcode, cmd) * 370 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:370 **return* 0 CalledProcessError: Command '['make', '-j8', 'all']' returned non-zero exit status 2. During handling of the above exception, another exception occurred: GeneratedCodeBuildException Traceback (most recent call last) Cell In[2], line 3 * 1 **# generate and build code* * 2 module_name_no_sfa, neuron_model_name_no_sfa **=** \ *----> 3 NESTCodeGeneratorUtils.generate_code_for("iaf_psc_alpha_neuron.nestml") File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:136, in NESTCodeGeneratorUtils.generate_code_for(cls, nestml_neuron_model, nestml_synapse_model, module_name, target_path, post_ports, mod_ports, codegen_opts, logging_level) * 133 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:133 uniq_id **=** **str**(uuid**.**uuid4()**.**hex) ** 134 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:134 module_name **=** **"**nestml_**"** **+** uniq_id **+** **"**_module**"** *--> 136 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:136 generate_nest_target(input_path=input_fns, * 137 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:137 install_path**=**install_path, ** 138 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:138 logging_level**=**logging_level, ** 139 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:139 module_name**=**module_name, ** 140 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:140 target_path**=**target_path, ** 141 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:141 suffix**=**"**_nestml**"**, ** 142 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:142 codegen_opts**=**_codegen_opts) ** 144 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:144 **if* nestml_synapse_model: * 145 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:145 **return* module_name, mangled_neuron_name, mangled_synapse_name File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:270, in generate_nest_target(input_path, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts) * 243 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:243 **def* generate_nest_target(input_path: Union[str, Sequence[str]], target_path: Optional[str] = None, * 244 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:244 install_path: Optional[**str**] **=** **None*, logging_level="ERROR", * 245 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:245 module_name**=**None*, store_log: bool = False, suffix: str = "", * 246 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:246 dev: **bool** **=** **False*, codegen_opts: Optional[Mapping[str, Any]] = None): * 247 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:247 ** **r**"""Generate and build code for NEST Simulator.* * 248 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:248 ** 249 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:249 ** Parameters* (...) * 268 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:268 ** A dictionary containing additional options for the target code generator.* * 269 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:269 ** """* --> 270 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:270 generate_target(input_path, target_platform="NEST", target_path=target_path, logging_level=logging_level, * 271 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:271 module_name**=**module_name, store_log**=**store_log, suffix**=**suffix, install_path**=**install_path, ** 272 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:272 dev**=**dev, codegen_opts**=**codegen_opts) File *~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:193, in generate_target(input_path, target_platform, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts) * 165 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:165 **r**"""Generate and build code for the given target platform.* * 166 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:166 ** 167 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:167 **Parameters* (...) * 188 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:188 ** A dictionary containing additional options for the target code generator.* * 189 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:189 **"""* * 191 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:191 configure_front_end(input_path, target_platform, target_path, install_path, logging_level, ** 192 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:192 module_name, store_log, suffix, dev, codegen_opts) *--> 193 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:193 if not process() == 0: * 194 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:194 **raise* Exception("Error(s) occurred while processing the model") File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:482, in process() * 480 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:480 **# perform build* * 481 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:481 **if* _builder is not None: --> 482 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:482 _builder.build() * 484 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:484 **if* FrontendConfiguration.store_log: * 485 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:485 store_log_to_file() File *~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:181, in NESTBuilder.build(self) * 177 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:177 subprocess**.**check_call(make_install_cmd, stderr**=**stderr, stdout**=**stdout, shell**=**shell, ** 178 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:178 cwd**=**str**(os**.**path**.**join(target_path))) ** 180 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:180 **except* subprocess.CalledProcessError as e: --> 181 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:181 raise GeneratedCodeBuildException(stages_exception[current_stage]) * 183 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:183 **finally*: * 184 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:184 **if* self._options["redirect"]:
On Tue, Sep 10, 2024 at 9:33 AM Anno Kurth a.kurth@fz-juelich.de wrote:
Hi Jona,
you might also be interested in the leaky integrate-and-fire model with adaptive threshold [https://nest-simulator.readthedocs.io/en/latest/models/mat2_psc_exp.html]. Here, the voltage is not reset after a threshold crossing, though.
Best
Anno
On 10.09.24 09:15, Charl Linssen wrote:
Hi Jona,
Thanks for writing in! Could the NESTML model(s) used in the tutorial at https://nestml.readthedocs.io/en/latest/tutorials/spike_frequency_adaptation... be what you're looking for? In general, it's easy to take a NESTML model (see https://nestml.readthedocs.io/en/latest/models_library/index.html) and add a threshold adaptation mechanism to it. Please let us know how you fare! (Please make sure you're using the latest NESTML, v8.0.0-rc1 or the GitHub master version.)
With kind regards, Charl
On Tue, Sep 10, 2024, at 08:09, jona.m.scholz@gmail.com wrote:
Hello everyone,
just a quick question in case anybody knows: is there a LIF model that has an adaptive spike threshold in NEST?
I know there's the GLIF model which can have a threshold, but it seems to bring other deviations from the conventional LIF model that I want to avoid. There's also the adaptive exponential integrate and fire model, but again I don't want the exponential part.
It's not a problem if no such model exists in NEST, I am only asking so I don't reimplement an existing model.
Any feedback would be appreciated.
Kind regards, Jona _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
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-- Anno Kurth Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience Jülich Research Centre Jülich, Germany
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 Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
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Hi Charl,
Thank you for the helpful response. It was exactly as you said and everything works now.
Have a nice weekend :)
Kind regards, Jona
On Fri, Sep 13, 2024 at 10:38 AM Charl Linssen nest-users@turingbirds.com wrote:
Ah, yes, that is indeed very informative. It indicates that the Boost C++ libraries are missing. Would it be possible for you to add Boost to the conda environment?
Perhaps you could check the full installation instructions for NESTML on Anaconda at: https://nestml.readthedocs.io/en/latest/installation.html#anaconda-installat...
Hope this helps! Charl
On Fri, Sep 13, 2024, at 09:41, Jona Scholz wrote:
Hi Charl,
The terminal logs are shown below. Is that the error message you were looking for?
Thanks for your help :)
Kind regards, Jona
CMake Warning (dev) at CMakeLists.txt:93 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it.
-- The CXX compiler identification is GNU 11.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /home/jona/miniconda3/envs/neuro/bin/x86_64-conda-linux-gnu-c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done
nestml_7f8d1ff3e3e8497da87659816759e61b_module Configuration Summary
C++ compiler : /home/jona/miniconda3/envs/neuro/bin/x86_64-conda-linux-gnu-c++ Build static libs : OFF C++ compiler flags : -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jona/miniconda3/envs/neuro/include NEST compiler flags : -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jona/miniconda3/envs/neuro/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/nest-simulator_1724732927678/work=/usr/local/src/conda/nest-simulator-3.8 -fdebug-prefix-map=/home/jona/miniconda3/envs/neuro=/usr/local/src/conda-prefix -lrt -std=c++17 -Wall -fopenmp -O2 -fdiagnostics-color=auto NEST include dirs : -I/home/jona/miniconda3/envs/neuro/include/nest -I/home/jona/miniconda3/envs/neuro/include -I/home/jona/miniconda3/envs/neuro/include -I/home/jona/miniconda3/envs/neuro/include -I/home/jona/miniconda3/envs/neuro/include NEST libraries flags : -L/home/jona/miniconda3/envs/neuro/lib/nest -lnest -lsli /home/jona/miniconda3/envs/neuro/x86_64-conda-linux-gnu/sysroot/usr/lib/libpthread.so
You can now build and install 'nestml_7f8d1ff3e3e8497da87659816759e61b_module' using make make install
The library file libnestml_7f8d1ff3e3e8497da87659816759e61b_module.so will be installed to /tmp/nestml_target_t1m_k1tx The module can be loaded into NEST using (nestml_7f8d1ff3e3e8497da87659816759e61b_module) Install (in SLI) nest.Install(nestml_7f8d1ff3e3e8497da87659816759e61b_module) (in PyNEST)
CMake Warning (dev) in CMakeLists.txt: No cmake_minimum_required command is present. A line of code such as
cmake_minimum_required(VERSION 3.30)should be added at the top of the file. The version specified may be lower if you wish to support older CMake versions for this project. For more information run "cmake --help-policy CMP0000". This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring done (3.7s) -- Generating done (0.0s) -- Build files have been written to: /home/jona/rstdp-gym/target [ 66%] Building CXX object CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/iaf_psc_alpha_neuron_nestml.o [ 66%] Building CXX object CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/nestml_7f8d1ff3e3e8497da87659816759e61b_module.o In file included from /home/jona/miniconda3/envs/neuro/include/nest/sort.h:36, from /home/jona/miniconda3/envs/neuro/include/nest/connector_base.h:35, from /home/jona/miniconda3/envs/neuro/include/nest/connection_manager.h:36, from /home/jona/miniconda3/envs/neuro/include/nest/connection_manager_impl.h:26, from /home/jona/rstdp-gym/target/nestml_7f8d1ff3e3e8497da87659816759e61b_module.cpp:26: /home/jona/miniconda3/envs/neuro/include/nest/iterator_pair.h:26:10: fatal error: boost/iterator/iterator_adaptor.hpp: No such file or directory 26 | #include <boost/iterator/iterator_adaptor.hpp> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. In file included from /home/jona/miniconda3/envs/neuro/include/nest/sort.h:36, from /home/jona/miniconda3/envs/neuro/include/nest/connector_base.h:35, from /home/jona/miniconda3/envs/neuro/include/nest/connection_manager.h:36, from /home/jona/miniconda3/envs/neuro/include/nest/kernel_manager.h:30, from /home/jona/rstdp-gym/target/iaf_psc_alpha_neuron_nestml.cpp:33: /home/jona/miniconda3/envs/neuro/include/nest/iterator_pair.h:26:10: fatal error: boost/iterator/iterator_adaptor.hpp: No such file or directory 26 | #include <boost/iterator/iterator_adaptor.hpp> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[2]: *** [CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/build.make:76: CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/nestml_7f8d1ff3e3e8497da87659816759e61b_module.o] Error 1 make[2]: *** Waiting for unfinished jobs.... make[2]: *** [CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/build.make:90: CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/iaf_psc_alpha_neuron_nestml.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:110: CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/all] Error 2 make: *** [Makefile:156: all] Error 2
On Thu, Sep 12, 2024 at 12:17 PM Charl Linssen nest-users@turingbirds.com wrote:
Hi Jona,
Sorry about the error. It might be related to the conda environment; the issue seems to be that there is an error during compilation, but the error message is not shown in these logs. Could you check in your terminal (that you used to launch the Jupyter notebook server) for the error messages from gcc?
Cheers, Charl
On Wed, Sep 11, 2024, at 22:06, Jona Scholz wrote:
Dear Charl and Anno,
Thank you for your replies.
I hadn't heard about neurons that don't reset and will have to look into it more. Thank you :)
I can't seem to run the SFA neuron tutorial linked in Charl's reply. It fails in the first call to NESTCodeGeneratorUtils.generate_code_for(...) with an error found below. I have tried it on two Ubuntu systems using NestML versions 8.0.0-rc1 and 8.0.0-rc2 with the iaf_psc_alpha_neuron.nestml model from the NestML master branch. It is probably just some technical problem on my end and I'm sure I will be able to resolve it soon. Nonetheless, if anyone spots something obvious in the error message below, please let me know.
Thanks for your help and have a great day!
Kind regards, Jona
The error message:
CalledProcessError Traceback (most recent call last) File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:174, in NESTBuilder.build(self) * 173 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:173 current_stage **=* *"**build**"* --> 174 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:174 subprocess.check_call(make_all_cmd, stderr=stderr, stdout=stdout, shell=shell,
- 175
https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:175 cwd**=**str**(os**.**path**.**join(target_path))) ** 176 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:176 current_stage **=* *"**install**"** File * ~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:369, in check_call(*popenargs, **kwargs) * 368 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:368 cmd **=** popenargs[**0**] *--> 369 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:369 raise CalledProcessError(retcode, cmd) * 370 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:370 **return* 0 CalledProcessError: Command '['make', '-j8', 'all']' returned non-zero exit status 2. During handling of the above exception, another exception occurred: GeneratedCodeBuildException Traceback (most recent call last) Cell In[2], line 3 * 1 **# generate and build code* * 2 module_name_no_sfa, neuron_model_name_no_sfa **=** \ *----> 3 NESTCodeGeneratorUtils.generate_code_for("iaf_psc_alpha_neuron.nestml") File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:136, in NESTCodeGeneratorUtils.generate_code_for(cls, nestml_neuron_model, nestml_synapse_model, module_name, target_path, post_ports, mod_ports, codegen_opts, logging_level) * 133 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:133 uniq_id **=* *str**(uuid**.**uuid4()**.**hex) ** 134 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:134 module_name **=* *"**nestml_**"* *+** uniq_id **+* *"**_module**"* --> 136 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:136 generate_nest_target(input_path=input_fns, * 137 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:137 install_path**=**install_path, ** 138 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:138 logging_level**=**logging_level, ** 139 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:139 module_name**=**module_name, ** 140 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:140 target_path**=**target_path, ** 141 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:141 suffix**=**"**_nestml**"**, ** 142 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:142 codegen_opts**=**_codegen_opts) ** 144 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:144 **if* nestml_synapse_model: * 145 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:145 **return* module_name, mangled_neuron_name, mangled_synapse_name File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:270, in generate_nest_target(input_path, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts) * 243 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:243 **def* generate_nest_target(input_path: Union[str, Sequence[str]], target_path: Optional[str] = None, * 244 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:244 install_path: Optional[**str**] **=* *None*, logging_level="ERROR", * 245 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:245 module_name**=**None*, store_log: bool = False, suffix: str = "", * 246 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:246 dev: **bool* *=* *False*, codegen_opts: Optional[Mapping[str, Any]] = None):
- 247
- *r**"""Generate and build code for NEST Simulator.* * 248
https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:248 ** 249 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:249 ** Parameters* (...) * 268 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:268 ** A dictionary containing additional options for the target code generator.* * 269 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:269 ** """* --> 270 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:270 generate_target(input_path, target_platform="NEST", target_path=target_path, logging_level=logging_level, * 271 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:271 module_name**=**module_name, store_log**=**store_log, suffix**=**suffix, install_path**=**install_path, ** 272 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:272 dev**=**dev, codegen_opts**=**codegen_opts) File * ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:193, in generate_target(input_path, target_platform, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts) * 165 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:165 **r**"""Generate and build code for the given target platform.* * 166 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:166 ** 167 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:167 **Parameters* (...) * 188 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:188 ** A dictionary containing additional options for the target code generator.* * 189 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:189 **"""* * 191 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:191 configure_front_end(input_path, target_platform, target_path, install_path, logging_level, ** 192 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:192 module_name, store_log, suffix, dev, codegen_opts) *--> 193 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:193 if not process() == 0: * 194 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:194 **raise* Exception("Error(s) occurred while processing the model") File ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:482, in process() * 480 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:480 **# perform build* * 481 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:481 **if* _builder is not None: --> 482 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:482 _builder.build() * 484 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:484 **if* FrontendConfiguration.store_log: * 485 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:485 store_log_to_file() File * ~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:181, in NESTBuilder.build(self) * 177 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:177 subprocess**.**check_call(make_install_cmd, stderr**=**stderr, stdout**=**stdout, shell**=**shell, ** 178 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:178 cwd**=**str**(os**.**path**.**join(target_path))) ** 180 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:180 **except* subprocess.CalledProcessError as e: --> 181 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:181 raise GeneratedCodeBuildException(stages_exception[current_stage]) * 183 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:183 **finally*: * 184 https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:184 **if* self._options["redirect"]:
On Tue, Sep 10, 2024 at 9:33 AM Anno Kurth a.kurth@fz-juelich.de wrote:
Hi Jona,
you might also be interested in the leaky integrate-and-fire model with adaptive threshold [https://nest-simulator.readthedocs.io/en/latest/models/mat2_psc_exp.html ]. Here, the voltage is not reset after a threshold crossing, though.
Best
Anno
On 10.09.24 09:15, Charl Linssen wrote:
Hi Jona,
Thanks for writing in! Could the NESTML model(s) used in the tutorial at
https://nestml.readthedocs.io/en/latest/tutorials/spike_frequency_adaptation... be what you're looking for? In general, it's easy to take a NESTML model (see https://nestml.readthedocs.io/en/latest/models_library/index.html) and add a threshold adaptation mechanism to it. Please let us know how you fare! (Please make sure you're using the latest NESTML, v8.0.0-rc1 or the GitHub master version.)
With kind regards, Charl
On Tue, Sep 10, 2024, at 08:09, jona.m.scholz@gmail.com wrote:
Hello everyone,
just a quick question in case anybody knows: is there a LIF model that has an adaptive spike threshold in NEST?
I know there's the GLIF model which can have a threshold, but it seems to bring other deviations from the conventional LIF model that I want to avoid. There's also the adaptive exponential integrate and fire model, but again I don't want the exponential part.
It's not a problem if no such model exists in NEST, I am only asking so I don't reimplement an existing model.
Any feedback would be appreciated.
Kind regards, Jona _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
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-- Anno Kurth Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience Jülich Research Centre Jülich, Germany
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 Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
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Anno Kurth -
Charl Linssen -
Jona Scholz -
jona.m.scholz＠gmail.com