sgkit icon indicating copy to clipboard operation
sgkit copied to clipboard

Set SGKIT_DISABLE_NUMBA_CACHE=1 by default

Open jeromekelleher opened this issue 1 year ago • 3 comments

This is causing persistent problems, with cryptic segfaults being really really hard to debug with Dask (I just lost a whole morning to it!).

We have to turn off the numba cache until this is sorted out somehow.

jeromekelleher avatar Dec 14 '23 12:12 jeromekelleher

Is changing the default in https://github.com/pystatgen/sgkit/blob/main/sgkit/accelerate.py#L6 sufficient?

tomwhite avatar Dec 18 '23 15:12 tomwhite

I guess a warning if numba cache is enabled also? It's a horrible gotcha.

jeromekelleher avatar Dec 18 '23 15:12 jeromekelleher

Partially addressed ion #1191.

To fully address I think we probably need to undocument this variable by removing the mention to it in the docs, and maybe add some comments in the source laying out the issue. Plus update to the changelog.

jeromekelleher avatar Feb 19 '24 16:02 jeromekelleher