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lazear / sage

Proteomics search & quantification so fast that it feels like magic
https://sage-docs.vercel.app
MIT License
201 stars 38 forks source link

fatal runtime error: stack overflow #131

Closed picciama closed 2 months ago

picciama commented 2 months ago

Hello @lazear ,

I encounter the following error:

thread '<unknown>' has overflowed its stack
fatal runtime error: stack overflow

This is happening on a big CPU node, when I run an unspecific digest with 240 CPUs in parallel, ~560 GB RAM consumption, with min_length=7 and max_length=20. It works with max_length=15 though. I wanted to sorta test how far I can go with the max peptide length.

While I can't pinpoint this to sth. specfiic, I think it may have to do with the stack being full since the fragment index is so huge already with the unspecific digest. Is it possible the stack runs into the heap?

I also know about #97 already and I am happy with a max length of 15 since most HLA-1 peptides fall within 8-12 aa length anyways... Just wanted to let you know that this error message can happen.

lazear commented 2 months ago

Thanks for the report - stay tuned for an update on the unspecific-digest front soon.

Your guess might be correct - some operating systems add guard pages to the stack boundary, and heap overflowing into the stack could cause a false stack overflow.