mrbuche
commented
1 week ago Fixed in #134.
$ cargo run -qr -F profile -- mesh -i spheres_resolution_4.npy -o target/foo.inp --smooth
automesh 0.1.10
Reading spheres_resolution_4.npy
Done 7.246989ms
Meshing target/foo.inp
⤷ Removed voxels 327.585084ms
Element-to-node connectivity 284.005907ms
Nodal coordinates 691.668606ms
Renumbered nodes 85.932201ms
Done 1.410858943s
Smoothing target/foo.inp
⤷ Node-to-element connectivity 489.889089ms
Node-to-node connectivity 5.430347083s
Nodal hierarchy 846.394093ms
Done 6.766705079s
Writing target/foo.inp
⤷ Nodal coordinates 4.626956897s
Element-to-node connectivity 3.780540771s
Done 9.124938823s 
hovey
Describe the bug
The calculation of the node-to-element connectivity appears to be much slower than other operations.
To Reproduce
$ cargo run -qr -F profile -- mesh -i spheres_resolution_2.npy -o target/foo.inp automesh 0.1.10 Reading spheres_resolution_2.npy Done 201.338µs Meshing target/foo.inp ⤷ Filter 3.053172ms Connectivity 1.756722ms Coordinates 5.495238ms Mapping 492.783µs Removal 61.794µs Renumbering 193.295µs Done 11.419183ms Smoothing target/foo.inp ⤷ Node-to-element connectivity 8.314554166s Node-to-node connectivity 26.056589ms Nodal hierarchy 7.161734ms Done 8.347809164s Writing target/foo.inp ⤷ Coordinates 34.842501ms Connectivity 24.634797ms Done 66.325293ms$ cargo run -qr -F profile -- mesh -i spheres_resolution_3.npy -o target/foo.inp automesh 0.1.10 Reading spheres_resolution_3.npy Done 487.264µs Meshing target/foo.inp ⤷ Filter 22.320514ms Connectivity 18.962217ms Coordinates 46.409529ms Mapping 2.836481ms Removal 558.733µs Renumbering 2.519586ms Done 95.556747ms Smoothing target/foo.inp ⤷ Node-to-element connectivity 768.169208482s Node-to-node connectivity 233.107442ms Nodal hierarchy 57.136488ms Done 768.459505013s Writing target/foo.inp ⤷ Coordinates 261.19101ms Connectivity 224.191682ms Done 551.462813msExpected behavior
Appears to be $O(N^2)$ rather than $O(N)$, which is likely due to looping over the element-to-node connectivity within the loop over the node-to-element connectivity in order to populate it.
Additional context
Reproduce using this commit. The node-to-element connectivity is currently needed to calculate the node-to-node connectivity and the nodal hierarchy.