Skip chunk coordinate enumeration in resize when array is only growing (#3650)#3702
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jakenotjay wants to merge 5 commits intozarr-developers:mainfrom
Open
Skip chunk coordinate enumeration in resize when array is only growing (#3650)#3702jakenotjay wants to merge 5 commits intozarr-developers:mainfrom
jakenotjay wants to merge 5 commits intozarr-developers:mainfrom
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d-v-b
approved these changes
Feb 11, 2026
rabernat
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Feb 11, 2026
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rabernat
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Great fix, but it needs a test, no?
…hunk enumeration skipped correctly
dcherian
approved these changes
Feb 11, 2026
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Motivation
Array.resize()enumerates all chunk coordinates ifdelete_outside_chunksisTrue(its default value), these old and new shapes are added into Python set objects to compute which chunks to delete. #3650 notes that this is totally unbounded in memory - even if the array is only growing and no chunks need deletion.In our case our array has approximately ~220 million chunks, and we want to add a new time step. Building these two sets of tuples explodes memory to >20GB and does not complete (at least deployed in a no-swap environment, I never left my laptop running long enough). Furthermore, the set difference will always be empty because growing a dimension can't produce chunks outside the new shape.
Fix
Rather than always checking which is O(total_chunks), first check if the new_shape is >= the dimensions of the old shape. If array is only growing, skip enumeration.
This is a targeted mitigation, rather than a complete solution to the problem described by 3650, a more complete solution would construct outside chunk coords from the shape diff, rather than naively enumerating all coords.
TODO:
docs/user-guide/*.mdchanges/