Out of memory when indexing a large fragment file #75

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opened 2025-10-14 17:05:36 -06:00 by navan · 0 comments

navan commented

2025-10-14 17:05:36 -06:00

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Originally created by @ValeryPolyakov on 9/17/2018

When I try to execute mmpdb index command on a large fragments file (>5M structures), Python runs out of memory even on a very big Linux node > 700Gb.

Can anything be done to process such big databases?

Thanks.

*Originally created by @ValeryPolyakov on 9/17/2018* When I try to execute _mmpdb index_ command on a large fragments file (>5M structures), Python runs out of memory even on a very big Linux node > 700Gb. Can anything be done to process such big databases? Thanks.