11 Sep
2024
11 Sep
'24
10:06 p.m.
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
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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
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r"""Generate and build code for NEST Simulator. 248
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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
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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
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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
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raise GeneratedCodeBuildException(stages_exception[current_stage]) 183
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finally: 184
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if self._options["redirect"]:
On Tue, Sep 10, 2024 at 9:33 AM Anno Kurth <a.kurth(a)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_adaptatio…
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(a)gmail.com wrote:
--
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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To unsubscribe send an email to users-leave(a)nest-simulator.org
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
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_______________________________________________
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To unsubscribe send an email to users-leave(a)nest-simulator.org