12 Sep
2024
12 Sep
'24
12:17 p.m.
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
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raise GeneratedCodeBuildException(stages_exception[current_stage]) * 183
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**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(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:
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
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
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
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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To unsubscribe send an email to users-leave(a)nest-simulator.org
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org