Fix non-PBC fake-cell sizing in get_neighborhood#1501
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The previous formula sized the fake cell as max(|positions|) * 5 * cutoff, which (a) depended on where the molecule sat relative to the origin rather than its actual extent, and (b) used a multiplicative safety margin instead of an additive one. A molecule with max|positions|=237 A and cutoff=5 produced a fake cell of ~5948 A per side. matscipy's neighbour_list then allocated a linked-cell grid of ~1.7 billion bins (~6 GiB CPU RAM) just to find a few hundred edges among ~50 atoms. In production this propagated into multi-hundred-GiB tensor allocations on accelerators and triggered uncatchable GPU page faults that took down 12 000-rank MPI runs. Replace with cell = extent + 5 * cutoff so the cell scales with the molecular bounding box and is translation-invariant. For a 200 A molecule the cell drops from ~6000 A to ~232 A; for a typical 10 A molecule from 250 A to ~35 A. Edge counts are unchanged; matscipy allocation goes from O(GiB) to O(MiB).
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this fixes the same issue as #1473 . are you happy with the fix there? |
Author
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Oh, yes, didn't see it. Thank you! |
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The previous formula sized the fake cell as
max(|positions|) * 5 * cutoff, which depended on where the molecule sat relative to the origin rather than its actual extent, and used a multiplicative safety margin instead of an additive one. A molecule with max|positions|=237 A and cutoff=5 produced a fake cell of ~5948 A per side. matscipy's neighbour_list then allocated a linked-cell grid of ~1.7 billion bins (~6 GiB CPU RAM) just to find a few hundred edges among ~50 atoms. In production this propagated into multi-hundred-GiB tensor allocations on accelerators and triggered uncatchable GPU page faults that took down 12 000-rank MPI runs.Replace with cell = extent + 5 * cutoff so the cell scales with the molecular bounding box and is translation-invariant. For a 200 A molecule the cell drops from ~6000 A to ~232 A; for a typical 10 A molecule from 250 A to ~35 A. Edge counts are unchanged; matscipy allocation goes from O(GiB) to O(MiB).
PS: I had out of memory errors for some geometries and opus4.7 found the bug and helped me patch.