biocore / biocore/BIRDMAn

Kernel dying at model comparison with no apparent reason

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Dominant language
Python
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Description

Dear all,

I have been trying to compare my model with a null model and although all the cells seem to run perfectly (no error messages) my kernel always dies when it comes to model comparison:

`import arviz as az`
`az.compare({"null": inference_null, "model": inference})`

A window with the following appears and I have no option but to loose everything that was already done:
Kernel Restarting
The kernel for birdman-analyses1/notebooks/modelotreatment.ipynb appears to have died. It will restart automatically.

I tried making more space free in my computer (about 350MB) and tried with different models, but still the same happens. The computer is a MacBook Pro with processor 2,3 GHz 8-Core Intel Core i9; 16 GB 2667 MHz DDR4; Ventura 13.5.
Does anyone know what could be happening here? I'm very thankful to any suggestion that might help me figure out what is the problem...

Following is a copy of my notebook with the code. Briefly, I am trying to compare gut microbiomes of tadpoles subject to the combinations of five different temperature treatments and three nitrate concentrations (= 15 treatments).

[modelocompleto.pdf](https://github.com/biocore/BIRDMAn/files/12388378/modelocompleto.pdf)

Also, the following appears at the terminal when the kernel is interrupted:
Restoring connection for e3e3d17e-e65f-49b9-a22d-bedf8a969edc:f6a62408-13a9-45f2-9550-898dc6e62b76
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.

Thank you very much!

Contributor guide

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Research direction

Start by reproducing the kernel restart at az.compare in notebooks/modelotreatment.ipynb, using the supplied model comparison code and modelocompleto.pdf as context. Trace the comparison step and its terminal output to identify the cause of the crash; done means documenting a reproducible cause and a verified resolution.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook, python
Domain
bioinformatics
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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