align_families.py: Kalign memory leak

galaxyproject / dunovo

Reference-free duplex sequencing pipeline.

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align_families.py: Kalign memory leak #7

Open NickSto opened 6 years ago

NickSto commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

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