PathlineFile.get_destination_pathline_data() performance

[wpbonelli]

The flopy3_modpath7_create_simulation.ipynb notebook is slow, taking 10-15 minutes on CI. The bottleneck seems to be in PathlineFile.get_destination_pathline_data(). Calculating pathline data for the backwards case with river cell locations is slowest. Computing endpoint data is generally fast.

Benchmark

Results from my machine (runtimes in milliseconds):

Name (time in ms)	Min	Max	Mean	StdDev	Median	IQR	Outliers	OPS	Rounds	Iterations
test_get_destination_endpoint_data[well-forward]	1.1320 (1.0)	1.6217 (1.02)	1.1668 (1.0)	0.0368 (1.20)	1.1588 (1.0)	0.0335 (1.38)	92;34	857.0405 (1.0)	790	1
test_get_destination_endpoint_data[river-forward]	1.2307 (1.09)	1.5880 (1.0)	1.2638 (1.08)	0.0308 (1.0)	1.2575 (1.09)	0.0242 (1.0)	82;62	791.2854 (0.92)	739	1
test_get_destination_endpoint_data[well-backward]	2.1071 (1.86)	37.6406 (23.70)	2.2844 (1.96)	1.8545 (60.22)	2.1728 (1.88)	0.0754 (3.11)	1;9	437.7543 (0.51)	366	1
test_get_destination_endpoint_data[river-backward]	2.1563 (1.90)	3.0739 (1.94)	2.2155 (1.90)	0.0620 (2.01)	2.2074 (1.90)	0.0526 (2.17)	33;16	451.3653 (0.53)	433	1
test_get_destination_pathline_data[well-backward]	26,589.8808 (>1000.0)	26,652.4284 (>1000.0)	26,623.4600 (>1000.0)	25.6051 (831.50)	26,616.2695 (>1000.0)	40.1569 (>1000.0)	2;0	0.0376 (0.00)	5	1
test_get_destination_pathline_data[well-forward]	40,028.3296 (>1000.0)	40,195.3408 (>1000.0)	40,104.5977 (>1000.0)	70.1838 (>1000.0)	40,077.0743 (>1000.0)	115.3085 (>1000.0)	2;0	0.0249 (0.00)	5	1
test_get_destination_pathline_data[river-forward]	61,112.0500 (>1000.0)	61,440.9841 (>1000.0)	61,247.5391 (>1000.0)	132.9419 (>1000.0)	61,200.5654 (>1000.0)	201.5238 (>1000.0)	2;0	0.0163 (0.00)	5	1
test_get_destination_pathline_data[river-backward]	568,730.0336 (>1000.0)	575,857.0278 (>1000.0)	571,281.7784 (>1000.0)	2,803.3254 (>1000.0)	571,121.0215 (>1000.0)	3,365.4625 (>1000.0)	1;0	0.0018 (0.00)	5	1

Performance profile

Below is a profile of the backward/river case. The ModpathFile.get_destination_pathline() method spends most of its time sorting numpy arrays:

Calls ordered by total time:

ncalls	tottime	percall	cumtime	percall filename:lineno(function)
2626	457.829	0.174	457.851	0.174 {method 'sort' of 'numpy.ndarray' objects}
2625	2.875	0.001	460.892	0.176 /Users/wes/dev/flopy/flopy/utils/modpathfile.py:129(get_data)
2627	0.158	0.000	0.182	0.000 {built-in method numpy.core._multiarray_umath.implement_array_function}
2	0.025	0.013	0.025	0.013 {built-in method numpy.array}
1	0.021	0.021	0.022	0.022 /Users/wes/dev/flopy/venv/lib/python3.10/site-packages/numpy/lib/arraysetops.py:523(in1d)
1	0.019	0.019	460.996	460.996 /Users/wes/dev/flopy/flopy/utils/modpathfile.py:195(get_destination_data)
1	0.018	0.018	0.018	0.018 {method 'copy' of 'numpy.ndarray' objects}
2625	0.017	0.000	0.022	0.000 /Users/wes/dev/flopy/venv/lib/python3.10/site-packages/numpy/core/_internal.py:395(_newnames)
2625	0.011	0.000	460.902	0.176 /Users/wes/dev/flopy/flopy/utils/modpathfile.py:633(get_data)
2625	0.008	0.000	0.167	0.000 <array_function internals>:177(where)
1	0.006	0.006	460.909	460.909 /Users/wes/dev/flopy/flopy/utils/modpathfile.py:266()
5273	0.003	0.000	0.003	0.000 {built-in method builtins.isinstance}
5250	0.002	0.000	0.002	0.000 {method 'remove' of 'list' objects}
1	0.002	0.002	460.997	460.997 /Users/wes/dev/flopy/flopy/utils/modpathfile.py:704(get_destination_pathline_data)

It looks like the sorting occurs in _ModpathSeries.get_data():

https://github.com/modflowpy/flopy/blob/5d0f5857d5ca5d5a92ad9207e0d8340acc214afa/flopy/utils/modpathfile.py#L150