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Published 20 hours ago • verified publisher icon galaxyproject

align_families.py: Kalign memory leak

Open NickSto opened this issue 7 years ago • 2 comments

In version 2.0.6.

The issue may be in the AlnStrs object allocated in the kalign C code and returned back to Python, which then may not properly free it.

NickSto avatar Oct 31 '17 17:10 NickSto

Update: 88b2e02 didn't fix this, but it reduced memory usage so that it's now very similar to MAFFT. Suggests it could be the same underlying issue, independent of the particular aligner.

NickSto avatar Nov 16 '17 01:11 NickSto

Idea: Maybe set maxtasksperchild on multiprocessing.Pool and see if replacing workers periodically helps.

NickSto avatar Jul 06 '18 05:07 NickSto