Kernel dying at model comparison with no apparent reason
- Dominant language
- Python
- Stars
- 25
- Forks
- 6
- PR merge metrics
- No merged PRs in 30d
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