Kernel crash when generating templates

[droumis]

Running the generate_templates_and_recordings.ipynb in a fresh env produces the error below and then kills the jupyter kernel.

Versions

Apple M1 Pro, macOS Ventura 13.5.2 Python 3.11.7 mearec 1.9.0 lfpy 2.3 neuron 8.2.3

Code from generate_templates_and_recordings.ipynb, setting njobs=1

import MEArec as Mr
default_info, mearec_home = mr.get_default_config()
cell_folder = default_info['cell_models_folder']
template_params = mr.get_default_templates_params()
template_params['n'] = 10
template_params['probe'] = 'Neuronexus-32'
tempgen = mr.gen_templates(cell_models_folder=cell_folder, params=template_params, n_jobs=1)

Error:

Intracellular simulation: /Users/droumis/.config/mearec/1.9.0/cell_models/bbp/L5_BP_bAC217_1
Warning: no DISPLAY environment variable.
--No graphics will be displayed.
NEURON: NaTs2_t is not a MECHANISM
 in biophysics.hoc near line 50
        insert NaTs2_t
                ^
        xopen("biophysics.hoc")
      execute1("{xopen("bi...")
    load_file(1, "biophysics.hoc")
NEURON: ProbGABAAB_EMS is not a template
 in synapses.hoc near line 274
             section.sec synapse = new ProbGABAAB_EMS(seg_x)
                                                           ^
        xopen("synapses.hoc")
      execute1("{xopen("sy...")
    load_file(1, "synapses/s...")

In the above, I'm setting n_jobs=1 because otherwise it tries to run with multiple jobs and I get a more cryptic error:

Current thread 0x00000001e559a080 (most recent call first):
  <no Python frame>
Fatal Python error: init_sys_streams: can't initialize sys standard streams
Python runtime state: core initialized
OSError: [Errno 9] Bad file descriptor

[droumis]

UPDATE: After some guess work, I seemed to have solved one of the issues by going to the ~/.config/mearec/1.9.0/cell_models/bbp/mods and running nrnivmodl. That seemed to resolve NEURON: NaTs2_t is not a MECHANISM. The rest of the notebook seems to be happy enough so I think I'll close this issue. I still can't use n_jobs>1 but I can live with that.

[alejoe91]

Ideally compilation should be done automatically at the first run, not sure why this didn't happen! Anyways, glad you figured this out ;)