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Use firedrake-rtree for spatial indexing#4981

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leo-collins wants to merge 41 commits intomainfrom
leo/rust-rstar
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Use firedrake-rtree for spatial indexing#4981
leo-collins wants to merge 41 commits intomainfrom
leo/rust-rstar

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@leo-collins leo-collins commented Mar 20, 2026 •
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Description

Use firedrake-rtree for spatial indexing.

  • This is an order of magnitude faster than libspatialindex for querying points.
  • We can now build a one dimensional spatial index, allowing us to remove a whole load of special-cased code.
  • We can now access the nodes of the tree and manually traverse it. This will be used to build a distributed rtree which will allow us to use sparse communication operations to build the VertexOnlyMesh, instead of the expensive allgathers we use currently.

leo-collins
leo-collins commented Mar 21, 2026
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connorjward
connorjward reviewed Mar 24, 2026
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connorjward
connorjward reviewed Mar 25, 2026
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@leo-collins leo-collins mentioned this pull request Mar 25, 2026
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@leo-collins leo-collins marked this pull request as ready for review March 26, 2026 18:33
connorjward
connorjward requested changes Mar 31, 2026
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Just tiny things. I think this is great and 99% ready.

firedrake/cython/rtree.pyx
size_t dim
RTreeError err

if coords_min.shape[0] != coords_max.shape[0] or coords_min.shape[1] != coords_max.shape[1]:
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Suggested change
if coords_min.shape[0] != coords_max.shape[0] or coords_min.shape[1] != coords_max.shape[1]:
if coords_min.shape != coords_max.shape:

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@leo-collins leo-collins Apr 2, 2026

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This doesn't work for some reason. coords_min.shape != coords_max.shape evaluates to true.

leo-collins added 21 commits April 2, 2026 11:06
@leo-collins
use rstar capi for cell location
8a07281
@leo-collins
add logging
85ae5e9
@leo-collins
remove allgather logs
5169948
@leo-collins
update comments
3b96b1e
@leo-collins
fix cached property
281c971
@leo-collins
merge logging
e8da836 
more logging
@leo-collins
more logs
ab58a9b
@leo-collins
more logging
8f7bd74
@leo-collins
adapt to new API
dcc3052
@leo-collins
rebase
1ffbc5d
@leo-collins
spatial index in 1D
94d0165
@leo-collins
partial fix
37a8a3f
@leo-collins
fix test
c7de8cd 
This test depended on the ordering of the candidate cells
returned by the rtree query. Instead we check the missing
coordinates correctly as suggested by the comment
@leo-collins
tidy up cython
e5722a0
@leo-collins
fixes
613c5f1
@leo-collins
renaming and use firedrake_rtree package
d1b9295
@leo-collins
firedrake-rtree fixes
c291d33
@leo-collins
remove unused stuff from rtree cython
dfe8df1
@leo-collins
free ids in error case
ebd96dc
@leo-collins
add firedrake-rtree dependency
470c1be 
add to build-requirements.txt
@leo-collins
remove unnecessary stuff from petschdr
c7eadf4
@leo-collins
fix docstrings
5395ca6 
docstrings

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@leo-collins @connorjward