Connectivity benchmarks cold-start

[cmdupuis3]

Closes #1632

Overview

This fix provides a bare-bones Grid that allows for properly cold timing of the connectivity benchmarks, aside from a numba warmup to remove that from timing results.

Example:

[50.00%] · For uxarray commit 5f0e401 <cmd/merge-OFE> (round 2/2):
[50.00%] ·· Benchmarking conda-py3.11-netcdf4-pip+pyfma-setuptools_scm-xarray
[75.00%] ··· bench_connectivity.Connectivity.time_edge_node ok
[75.00%] ··· ============ ==========
resolution
------------ ----------
480km 1.27±0ms
120km 3.99±0ms
30km 100±0ms
15km 434±0ms
7.5km 1.97±0s
3.75km 9.92±0s
============ ==========

PR Checklist

General

• An issue is created and linked
• Added appropriate labels (if your uxarray repo permissions allow it)
• Filled out Overview and Expected Usage (if applicable) sections

Testing & Benchmarking

• Adequate tests are created if there is new functionality
• Tests are not too basic (such as simply calling a function and nothing else)
• Tests cover all major paths in your new functions
• If this PR could affect performance, ran ASV benchmarks and confirmed they show expected behavior (add a new benchmark if necessary)

Documentation

• Docstrings have been added to all new functions
• Docstrings have been updated with any function changes

[github-actions]

ASV Benchmarking

Benchmark Comparison Results

Benchmarks that have improved:

Change	Before [b1436fb]	After [9da2b14]	Ratio	Benchmark (Parameter)
-	521M	338M	0.65	face_bounds.FaceBounds.peakmem_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/ugrid/geoflow-small/grid.nc'))
-	631M	335M	0.53	face_bounds.FaceBounds.peakmem_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/ugrid/quad-hexagon/grid.nc'))
-	452M	329M	0.73	mpas_ocean.Gradient.peakmem_gradient('480km')

Benchmarks that have stayed the same:

Change	Before [b1436fb]	After [9da2b14]	Ratio	Benchmark (Parameter)
	243±10ms	239±7ms	0.99	bench_connectivity.Connectivity.time_edge_face('120km')
	14.0±0.6ms	13.5±0.08ms	0.96	bench_connectivity.Connectivity.time_edge_face('480km')
	230±0.3ms	231±0.5ms	1.00	bench_connectivity.Connectivity.time_edge_node('120km')
	12.6±0.07ms	12.6±0.05ms	1.00	bench_connectivity.Connectivity.time_edge_node('480km')
	231±0.7ms	230±0.6ms	1.00	bench_connectivity.Connectivity.time_face_edge('120km')
	12.9±0.07ms	12.9±0.05ms	1.00	bench_connectivity.Connectivity.time_face_edge('480km')
	829±5ms	827±6ms	1.00	bench_connectivity.Connectivity.time_face_face('120km')
	51.0±0.4ms	50.9±0.3ms	1.00	bench_connectivity.Connectivity.time_face_face('480km')
	59.7±0.8μs	60.0±1μs	1.00	bench_connectivity.Connectivity.time_face_node('120km')
	57.8±0.9μs	57.8±0.9μs	1.00	bench_connectivity.Connectivity.time_face_node('480km')
	376±8μs	379±6μs	1.01	bench_connectivity.Connectivity.time_n_nodes_per_face('120km')
	313±10μs	300±6μs	0.96	bench_connectivity.Connectivity.time_n_nodes_per_face('480km')
	232±0.2ms	233±0.3ms	1.00	bench_connectivity.Connectivity.time_node_edge('120km')
	13.2±0.2ms	13.1±0.07ms	0.99	bench_connectivity.Connectivity.time_node_edge('480km')
	79.2±2ms	79.1±0.6ms	1.00	bench_connectivity.Connectivity.time_node_face('120km')
	4.89±0.03ms	4.85±0.04ms	0.99	bench_connectivity.Connectivity.time_node_face('480km')
	335M	334M	1.00	face_bounds.FaceBounds.peakmem_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/mpas/QU/oQU480.231010.nc'))
	363M	365M	1.01	face_bounds.FaceBounds.peakmem_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/scrip/outCSne8/outCSne8.nc'))
	20.5±0.08μs	20.3±0.1μs	0.99	face_bounds.FaceBounds.time_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/mpas/QU/oQU480.231010.nc'))
	9.76±0.08μs	9.64±0.05μs	0.99	face_bounds.FaceBounds.time_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/scrip/outCSne8/outCSne8.nc'))
	9.42±0.1ms	9.46±0.07ms	1.00	face_bounds.FaceBounds.time_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/ugrid/geoflow-small/grid.nc'))
	1.93±0.05ms	1.96±0.03ms	1.02	face_bounds.FaceBounds.time_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/ugrid/quad-hexagon/grid.nc'))
	931±6ns	938±3ns	1.01	geometry_kernels.AccucrossKernels.time_accucross
	2.39±0.01μs	2.34±0μs	0.98	geometry_kernels.AccucrossKernels.time_accucross_pair
	268±0.7ns	276±10ns	1.03	geometry_kernels.EFTPrimitives.time_acc_sqrt_re
	262±1ns	262±0.6ns	1.00	geometry_kernels.EFTPrimitives.time_diff_of_products
	214±1ns	212±2ns	0.99	geometry_kernels.EFTPrimitives.time_two_prod
	212±0.6ns	214±1ns	1.01	geometry_kernels.EFTPrimitives.time_two_sum
	1.15±0μs	1.17±0.01μs	1.01	geometry_kernels.GCAConstLatIntersection.time_accux_constlat_kernel
	847±2ns	850±9ns	1.00	geometry_kernels.GCAConstLatIntersection.time_gca_const_lat_intersection
	1.54±0μs	1.55±0μs	1.01	geometry_kernels.GCAConstLatIntersection.time_try_gca_const_lat_intersection
	1.27±0μs	1.27±0μs	1.01	geometry_kernels.GCAGCAIntersection.time_accux_gca_kernel
	1.11±0μs	1.10±0μs	0.99	geometry_kernels.GCAGCAIntersection.time_gca_gca_intersection
	1.82±0.02μs	1.80±0.01μs	0.99	geometry_kernels.GCAGCAIntersection.time_try_gca_gca_intersection
	38.5±0.02μs	38.3±0.3μs	1.00	geometry_kernels.OrientPredicates.time_on_minor_arc
	472±2ns	467±1ns	0.99	geometry_kernels.OrientPredicates.time_orient3d_on_sphere
	2.92±0.1ms	2.79±0ms	0.95	geometry_samebody.SameBodyConstLat.time_accux_dispatch
	1.33±0ms	1.33±0ms	1.00	geometry_samebody.SameBodyConstLat.time_accux_kernel
	1.79±0.01ms	1.78±0.01ms	0.99	geometry_samebody.SameBodyConstLat.time_fp64_dispatch
	151±0.2μs	151±0.7μs	1.00	geometry_samebody.SameBodyConstLat.time_fp64_kernel
	32.7±0.3ms	32.7±0.2ms	1.00	geometry_samebody_gcagca.SameBodyGcaGca.time_accux_dispatch
	10.7±0.01ms	10.7±0.04ms	0.99	geometry_samebody_gcagca.SameBodyGcaGca.time_accux_kernel
	28.0±0.1ms	31.4±4ms	~1.12	geometry_samebody_gcagca.SameBodyGcaGca.time_fp64_dispatch
	4.45±0.02ms	4.43±0.01ms	1.00	geometry_samebody_gcagca.SameBodyGcaGca.time_fp64_kernel
	781±4ms	782±2ms	1.00	import.Imports.timeraw_import_uxarray
	912±10ns	908±10ns	1.00	mpas_ocean.CheckNorm.time_check_norm('120km')
	853±10ns	853±20ns	1.00	mpas_ocean.CheckNorm.time_check_norm('480km')
	722±5ms	718±5ms	0.99	mpas_ocean.ConnectivityConstruction.time_face_face_connectivity('120km')
	44.8±0.2ms	45.3±0.5ms	1.01	mpas_ocean.ConnectivityConstruction.time_face_face_connectivity('480km')
	13.5±0.05μs	13.5±0.08μs	1.00	mpas_ocean.ConnectivityConstruction.time_n_nodes_per_face('120km')
	13.6±0.1μs	13.6±0.05μs	1.00	mpas_ocean.ConnectivityConstruction.time_n_nodes_per_face('480km')
	4.54±0.01ms	4.56±0.03ms	1.01	mpas_ocean.ConstructFaceLatLon.time_cartesian_averaging('120km')
	3.00±0.02ms	2.99±0.01ms	1.00	mpas_ocean.ConstructFaceLatLon.time_cartesian_averaging('480km')
	3.31±0.01s	3.31±0.01s	1.00	mpas_ocean.ConstructFaceLatLon.time_welzl('120km')
	213±0.5ms	213±2ms	1.00	mpas_ocean.ConstructFaceLatLon.time_welzl('480km')
	19.7±0.03ms	19.7±0.02ms	1.00	mpas_ocean.ConstructTreeStructures.time_ball_tree('120km')
	1.12±0.01ms	1.09±0.01ms	0.98	mpas_ocean.ConstructTreeStructures.time_ball_tree('480km')
	10.6±0.01ms	10.6±0.01ms	1.00	mpas_ocean.ConstructTreeStructures.time_kd_tree('120km')
	748±7μs	736±7μs	0.98	mpas_ocean.ConstructTreeStructures.time_kd_tree('480km')
	659±2ms	648±0.8ms	0.98	mpas_ocean.CrossSections.time_const_lat('120km', 1)
	328±2ms	331±3ms	1.01	mpas_ocean.CrossSections.time_const_lat('120km', 2)
	171±2ms	170±0.6ms	1.00	mpas_ocean.CrossSections.time_const_lat('120km', 4)
	483±1ms	489±6ms	1.01	mpas_ocean.CrossSections.time_const_lat('480km', 1)
	247±2ms	247±2ms	1.00	mpas_ocean.CrossSections.time_const_lat('480km', 2)
	126±0.3ms	126±0.5ms	1.00	mpas_ocean.CrossSections.time_const_lat('480km', 4)
	22.4±0.5ms	22.1±0.06ms	0.99	mpas_ocean.DualMesh.time_dual_mesh_construction('120km')
	2.57±0.02ms	2.57±0.02ms	1.00	mpas_ocean.DualMesh.time_dual_mesh_construction('480km')
	836±2ms	844±3ms	1.01	mpas_ocean.GeoDataFrame.time_to_geodataframe('120km', False)
	50.2±0.6ms	50.7±0.4ms	1.01	mpas_ocean.GeoDataFrame.time_to_geodataframe('120km', True)
	73.3±0.6ms	72.2±0.5ms	0.98	mpas_ocean.GeoDataFrame.time_to_geodataframe('480km', False)
	5.65±0.07ms	5.52±0.1ms	0.98	mpas_ocean.GeoDataFrame.time_to_geodataframe('480km', True)
	350M	350M	1.00	mpas_ocean.Gradient.peakmem_gradient('120km')
	165±0.2ms	166±2ms	1.01	mpas_ocean.Gradient.time_gradient('120km')
	12.0±0.4ms	11.5±0.08ms	0.96	mpas_ocean.Gradient.time_gradient('480km')
	188±1μs	188±0.4μs	1.00	mpas_ocean.HoleEdgeIndices.time_construct_hole_edge_indices('120km')
	87.7±0.4μs	87.3±0.6μs	1.00	mpas_ocean.HoleEdgeIndices.time_construct_hole_edge_indices('480km')
	350M	350M	1.00	mpas_ocean.Integrate.peakmem_integrate('120km')
	329M	329M	1.00	mpas_ocean.Integrate.peakmem_integrate('480km')
	180±1μs	180±1μs	1.00	mpas_ocean.Integrate.time_integrate('120km')
	157±0.8μs	156±0.7μs	1.00	mpas_ocean.Integrate.time_integrate('480km')
	187±2ms	189±1ms	1.01	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('120km', 'exclude')
	188±2ms	187±0.6ms	1.00	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('120km', 'include')
	188±1ms	188±0.7ms	1.00	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('120km', 'split')
	13.9±0.2ms	14.0±0.2ms	1.01	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('480km', 'exclude')
	13.9±0.06ms	14.2±0.07ms	1.02	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('480km', 'include')
	13.9±0.05ms	14.0±0.2ms	1.00	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('480km', 'split')
	281±2μs	283±1μs	1.01	mpas_ocean.PointInPolygon.time_face_search_lonlat('120km')
	286±0.8μs	286±1μs	1.00	mpas_ocean.PointInPolygon.time_face_search_lonlat('480km')
	268±1μs	266±2μs	0.99	mpas_ocean.PointInPolygon.time_face_search_xyz('120km')
	267±1μs	269±2μs	1.01	mpas_ocean.PointInPolygon.time_face_search_xyz('480km')
	211±0.4ms	212±1ms	1.00	mpas_ocean.RemapDownsample.time_bilinear_remapping
	227±2ms	228±0.4ms	1.00	mpas_ocean.RemapDownsample.time_inverse_distance_weighted_remapping
	4.28±0.02ms	4.31±0.01ms	1.01	mpas_ocean.RemapDownsample.time_nearest_neighbor_remapping
	1.18±0s	1.18±0s	1.00	mpas_ocean.RemapUpsample.time_bilinear_remapping
	36.0±0.4ms	36.0±0.2ms	1.00	mpas_ocean.RemapUpsample.time_inverse_distance_weighted_remapping
	8.82±0.2ms	8.93±0.2ms	1.01	mpas_ocean.RemapUpsample.time_nearest_neighbor_remapping
	27.0±0.4ms	27.1±0.3ms	1.00	mpas_ocean.ZonalAverage.time_zonal_average('120km')
	5.31±0.06ms	5.47±0.05ms	1.03	mpas_ocean.ZonalAverage.time_zonal_average('480km')
	325M	324M	1.00	quad_hexagon.QuadHexagon.peakmem_open_dataset
	324M	324M	1.00	quad_hexagon.QuadHexagon.peakmem_open_grid
	6.51±0.07ms	6.48±0.2ms	1.00	quad_hexagon.QuadHexagon.time_open_dataset
	5.53±0.1ms	5.51±0.1ms	1.00	quad_hexagon.QuadHexagon.time_open_grid

[Sevans711]

Looks like a clean fix for these benchmarks. The run-benchmark results, along with the results reported in original message in PR thread, now all show expected scaling with grid size, rather than microsecond times regardless of grid size.

I considered whether it would make more sense to use Grid.__init__ with a dataset made up of just source_grid.node_lon, source_grid.node_lat, source_grid.face_node_connectivity, instead of using Grid.from_topology(), but then I realized that it shouldn't affect the timing of the benchmarks themselves, because that all happens directly in setup(), anyways.

So, looks good to me, no notes, my recommendation is to merge to main!