clinssen
commented
2 years ago Hi, thanks for your error report. This is an error we were seeing earlier on MacOS systems, which was caused when a script was calling generate_nest_target() without this call being enclosed in an if __name__ == "__main__" block. But it would be strange if this was also happening from within Jupyter notebooks.
Could you check that you are running the latest version of NESTML (optionally, do a pip install git+https://github.com/nest/nestml --upgrade)?
@pnbabu: could you see if you can replicate this error, as you also have a Mac system?
ewa8
Hi, I tried running the following code from the NESTML dopamine-modulated STDP synapse tutorial with my own neuron module (which I have previously tested and can be compiled and installed in NEST):
module_name, neuron_model_name, synapse_model_name = \ generate_code_for("nest_module/snr.nestml", "nest_module/neuromodulated_stdp.nestml", post_ports=["post_spikes"], mod_ports=["mod_spikes"])and I got the following error:
nestml_180c32c25bde495cbc0827e3b7a400b9_module Configuration Summary
C++ compiler : /usr/bin/clang++ Build static libs : OFF C++ compiler flags : NEST compiler flags : -O2 -std=c++11 -Wall -Xclang -fopenmp -O3 -DNDEBUG ... 14 warnings and 2 errors generated. make[2]: [CMakeFiles/nestml_180c32c25bde495cbc0827e3b7a400b9_module_module.dir/nestml_180c32c25bde495cbc0827e3b7a400b9_module.o] Error 1 make[1]: [CMakeFiles/nestml_180c32c25bde495cbc0827e3b7a400b9_module_module.dir/all] Error 2 make: *** [all] Error 2 Output exceeds the size limit. Open the full output data in a text editor CalledProcessError Traceback (most recent call last) File /opt/homebrew/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:151, in NESTBuilder.build(self) 150 try: --> 151 subprocess.check_call(make_all_cmd, stderr=subprocess.STDOUT, shell=shell, 152 cwd=str(os.path.join(target_path))) 153 except subprocess.CalledProcessError as e:
File /opt/homebrew/Cellar/python@3.10/3.10.2/Frameworks/Python.framework/Versions/3.10/lib/python3.10/subprocess.py:369, in check_call(*popenargs, **kwargs) 368 cmd = popenargs[0] --> 369 raise CalledProcessError(retcode, cmd) 370 return 0
CalledProcessError: Command '['make', 'all']' returned non-zero exit status 2.
During handling of the above exception, another exception occurred:
GeneratedCodeBuildException Traceback (most recent call last) /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/01 - General behaviour.ipynb Cell 7 in <cell line: 3>() 1 # generate and build code 2 module_name, neuron_model_name, synapse_model_name = \ ----> 3 generate_code_for("nest_module/snr.nestml", 4 "nest_module/neuromodulated_stdp.nestml", 5 post_ports=["post_spikes"], 6 mod_ports=["mod_spikes"]) ... --> 154 raise GeneratedCodeBuildException('Error occurred during \'make all\'! More detailed error messages can be found in stdout.') 156 # finally execute make install 157 try:
GeneratedCodeBuildException: Error occurred during 'make all'! More detailed error messages can be found in stdout.
Additionally, I tried running the code with the iaf_psc_delta neuron model just like it is shown in the tutorial to make sure it is not my neuron model throwing the error but I just got this error instead:
Exception Traceback (most recent call last) /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/01 - General behaviour.ipynb Cell 7 in <cell line: 3>() 1 # generate and build code 2 module_name, neuron_model_name, synapse_model_name = \ ----> 3 generate_code_for(iaf_psc_delta, 4 "nest_module/neuromodulated_stdp.nestml", 5 post_ports=["post_spikes"], 6 mod_ports=["mod_spikes"])
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/01 - General behaviour.ipynb Cell 7 in generate_code_for(nestml_neuron_model, nestml_synapse_model, post_ports, mod_ports, uniq_id, logging_level) 51 # generate the code for neuron and synapse (co-generated) 52 modulename = "nestml" + uniq_id + "_module" ---> 53 generate_nest_target(input_path=[neuron_uniq_fn, synapse_uniq_fn], 54 logging_level=logging_level, 55 module_name=module_name, 56 suffix="_nestml", 57 codegen_opts={"neuron_parent_class": "StructuralPlasticityNode", 58 "neuron_parent_class_include": "structural_plasticity_node.h", 59 "neuron_synapse_pairs": [{"neuron": neuron_model_name_uniq, 60 "synapse": synapse_model_name_uniq, 61 "post_ports": post_ports, 62 "vt_ports": mod_ports}]}) 63 mangled_neuron_name = neuron_model_name_uniq + "_nestml_with" + synapse_model_name_uniq + "_nestml" 64 mangled_synapse_name = synapse_model_name_uniq + "_nestml_with" + neuron_model_name_uniq + "_nestml" ... --> 432 raise Exception("Neuron name used in pair ("" + neuron_name + "") not found") # XXX: log error 433 return neurons, synapses 434 neuron = neurons[neuron_names.index(neuron_name + FrontendConfiguration.suffix)]
Exception: Neuron name used in pair ( + neuron_name + ) not found
Any idea what it might be caused by or how I could otherwise compile the STDP synapse with my neuron model?