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: 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.) -- 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

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 &lt;a.kurth(a)fz-juelich.de&gt; 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: 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.) -- 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 _______________________________________________ NEST Users mailing list -- users(a)nest-simulator.org 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

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-installa… 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 &lt;nest-users(a)turingbirds.com&gt; 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 &lt;a.kurth(a)fz-juelich.de&gt; 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: 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.) -- 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 _______________________________________________ NEST Users mailing list -- users(a)nest-simulator.org 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 _______________________________________________ NEST Users mailing list -- users(a)nest-simulator.org 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