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Improve the computation of TreeSet#228

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gdalle merged 3 commits intomainfrom
acyclic_tree
Apr 4, 2025
Merged

Improve the computation of TreeSet#228
gdalle merged 3 commits intomainfrom
acyclic_tree

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@amontoison amontoison commented Apr 2, 2025

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@amontoison amontoison added performance Speeding things up benchmark Run benchmarks on PR labels Apr 2, 2025
@amontoison amontoison requested a review from gdalle April 2, 2025 23:57
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codecov bot commented Apr 3, 2025 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (ba7da77) to head (d02912a).
Report is 1 commits behind head on main.

Additional details and impacted files 
@@            Coverage Diff            @@
##              main      #228   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           15        15           
  Lines         1758      1784   +26     
=========================================
+ Hits          1758      1784   +26

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github-actions bot commented Apr 3, 2025 •
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Benchmark Results

main 6739849... main/67398491447fb4...
coloring/nonsymmetric/bidirectional/direct/n=1000/p=0.002 1.92 ± 0.012 ms 1.93 ± 0.013 ms 0.997
coloring/nonsymmetric/bidirectional/direct/n=1000/p=0.005 4.4 ± 0.032 ms 4.4 ± 0.031 ms 1
coloring/nonsymmetric/bidirectional/direct/n=1000/p=0.01 9.93 ± 0.084 ms 9.86 ± 0.068 ms 1.01
coloring/nonsymmetric/bidirectional/direct/n=100000/p=0.0001 2.27 ± 0.048 s 2.3 ± 0.036 s 0.989
coloring/nonsymmetric/bidirectional/direct/n=100000/p=2.0e-5 0.298 ± 0.016 s 0.302 ± 0.0071 s 0.989
coloring/nonsymmetric/bidirectional/direct/n=100000/p=5.0e-5 0.876 ± 0.01 s 0.882 ± 0.031 s 0.993
coloring/nonsymmetric/bidirectional/substitution/n=1000/p=0.002 6.04 ± 1.2 ms 5.36 ± 1.1 ms 1.13
coloring/nonsymmetric/bidirectional/substitution/n=1000/p=0.005 14.1 ± 0.81 ms 13.2 ± 0.87 ms 1.07
coloring/nonsymmetric/bidirectional/substitution/n=1000/p=0.01 31.3 ± 1.1 ms 29.6 ± 0.27 ms 1.06
coloring/nonsymmetric/bidirectional/substitution/n=100000/p=0.0001 7.05 s 6.94 s 1.02
coloring/nonsymmetric/bidirectional/substitution/n=100000/p=2.0e-5 0.996 ± 0.047 s 0.849 ± 0.015 s 1.17
coloring/nonsymmetric/bidirectional/substitution/n=100000/p=5.0e-5 2.98 ± 0.21 s 2.76 ± 0.069 s 1.08
coloring/nonsymmetric/column/direct/n=1000/p=0.002 0.486 ± 0.011 ms 0.49 ± 0.011 ms 0.993
coloring/nonsymmetric/column/direct/n=1000/p=0.005 1.2 ± 0.015 ms 1.21 ± 0.01 ms 0.995
coloring/nonsymmetric/column/direct/n=1000/p=0.01 3.03 ± 0.32 ms 3.31 ± 0.33 ms 0.914
coloring/nonsymmetric/column/direct/n=100000/p=0.0001 0.528 ± 0.016 s 0.535 ± 0.013 s 0.988
coloring/nonsymmetric/column/direct/n=100000/p=2.0e-5 0.0811 ± 0.00059 s 0.082 ± 0.0021 s 0.988
coloring/nonsymmetric/column/direct/n=100000/p=5.0e-5 0.205 ± 0.0024 s 0.206 ± 0.0028 s 0.994
coloring/nonsymmetric/row/direct/n=1000/p=0.002 0.483 ± 0.011 ms 0.481 ± 0.01 ms 1
coloring/nonsymmetric/row/direct/n=1000/p=0.005 1.21 ± 0.013 ms 1.21 ± 0.01 ms 0.999
coloring/nonsymmetric/row/direct/n=1000/p=0.01 3.06 ± 0.016 ms 3.07 ± 0.017 ms 0.999
coloring/nonsymmetric/row/direct/n=100000/p=0.0001 0.539 ± 0.016 s 0.546 ± 0.0047 s 0.986
coloring/nonsymmetric/row/direct/n=100000/p=2.0e-5 0.082 ± 0.001 s 0.0829 ± 0.00098 s 0.989
coloring/nonsymmetric/row/direct/n=100000/p=5.0e-5 0.205 ± 0.0029 s 0.212 ± 0.0025 s 0.966
coloring/symmetric/column/direct/n=1000/p=0.002 1.02 ± 0.0099 ms 1.02 ± 0.0079 ms 1.01
coloring/symmetric/column/direct/n=1000/p=0.005 2.27 ± 0.019 ms 2.26 ± 0.013 ms 1
coloring/symmetric/column/direct/n=1000/p=0.01 4.93 ± 0.03 ms 4.9 ± 0.028 ms 1.01
coloring/symmetric/column/direct/n=100000/p=0.0001 0.817 ± 0.019 s 0.852 ± 0.027 s 0.959
coloring/symmetric/column/direct/n=100000/p=2.0e-5 0.146 ± 0.00078 s 0.145 ± 0.0015 s 1
coloring/symmetric/column/direct/n=100000/p=5.0e-5 0.334 ± 0.0061 s 0.345 ± 0.0082 s 0.969
coloring/symmetric/column/substitution/n=1000/p=0.002 3.15 ± 0.24 ms 2.84 ± 0.73 ms 1.11
coloring/symmetric/column/substitution/n=1000/p=0.005 7.55 ± 0.69 ms 6.69 ± 0.1 ms 1.13
coloring/symmetric/column/substitution/n=1000/p=0.01 15.8 ± 0.5 ms 14.7 ± 0.14 ms 1.08
coloring/symmetric/column/substitution/n=100000/p=0.0001 3.18 ± 0.13 s 2.99 ± 0.0043 s 1.07
coloring/symmetric/column/substitution/n=100000/p=2.0e-5 0.446 ± 0.027 s 0.405 ± 0.018 s 1.1
coloring/symmetric/column/substitution/n=100000/p=5.0e-5 1.24 ± 0.1 s 1.18 ± 0.057 s 1.06
decompress/nonsymmetric/bidirectional/direct/n=1000/p=0.002 0.143 ± 0.004 ms 0.145 ± 0.004 ms 0.986
decompress/nonsymmetric/bidirectional/direct/n=1000/p=0.005 0.23 ± 0.0091 ms 0.234 ± 0.0087 ms 0.985
decompress/nonsymmetric/bidirectional/direct/n=1000/p=0.01 0.375 ± 0.011 ms 0.374 ± 0.013 ms 1
decompress/nonsymmetric/bidirectional/direct/n=100000/p=0.0001 0.0934 ± 0.0027 s 0.0957 ± 0.0038 s 0.976
decompress/nonsymmetric/bidirectional/direct/n=100000/p=2.0e-5 31.5 ± 0.86 ms 0.0342 ± 0.0017 s 0.922
decompress/nonsymmetric/bidirectional/direct/n=100000/p=5.0e-5 0.0577 ± 0.00088 s 0.0629 ± 0.00077 s 0.918
decompress/nonsymmetric/bidirectional/substitution/n=1000/p=0.002 0.159 ± 0.0065 ms 0.152 ± 0.0064 ms 1.05
decompress/nonsymmetric/bidirectional/substitution/n=1000/p=0.005 0.312 ± 0.01 ms 0.317 ± 0.01 ms 0.985
decompress/nonsymmetric/bidirectional/substitution/n=1000/p=0.01 0.61 ± 0.015 ms 0.628 ± 0.013 ms 0.971
decompress/nonsymmetric/bidirectional/substitution/n=100000/p=0.0001 0.197 ± 0.0046 s 0.198 ± 0.0063 s 0.997
decompress/nonsymmetric/bidirectional/substitution/n=100000/p=2.0e-5 0.0368 ± 0.00085 s 0.0354 ± 0.0008 s 1.04
decompress/nonsymmetric/bidirectional/substitution/n=100000/p=5.0e-5 0.0928 ± 0.013 s 0.0806 ± 0.0023 s 1.15
decompress/nonsymmetric/column/direct/n=1000/p=0.002 26.4 ± 1.3 μs 27.8 ± 1.1 μs 0.947
decompress/nonsymmetric/column/direct/n=1000/p=0.005 0.05 ± 0.0018 ms 0.0511 ± 0.0016 ms 0.979
decompress/nonsymmetric/column/direct/n=1000/p=0.01 0.0907 ± 0.004 ms 0.0901 ± 0.0035 ms 1.01
decompress/nonsymmetric/column/direct/n=100000/p=0.0001 26.7 ± 1.7 ms 27.9 ± 0.73 ms 0.955
decompress/nonsymmetric/column/direct/n=100000/p=2.0e-5 4.84 ± 0.53 ms 4.94 ± 0.28 ms 0.98
decompress/nonsymmetric/column/direct/n=100000/p=5.0e-5 12.6 ± 0.35 ms 12.9 ± 0.42 ms 0.982
decompress/nonsymmetric/row/direct/n=1000/p=0.002 24.1 ± 1.5 μs 26 ± 1.2 μs 0.928
decompress/nonsymmetric/row/direct/n=1000/p=0.005 0.0429 ± 0.0016 ms 0.0458 ± 0.0032 ms 0.937
decompress/nonsymmetric/row/direct/n=1000/p=0.01 0.0775 ± 0.0034 ms 0.079 ± 0.0032 ms 0.981
decompress/nonsymmetric/row/direct/n=100000/p=0.0001 11.6 ± 2.1 ms 12.2 ± 0.62 ms 0.957
decompress/nonsymmetric/row/direct/n=100000/p=2.0e-5 3.28 ± 0.16 ms 3.37 ± 0.18 ms 0.975
decompress/nonsymmetric/row/direct/n=100000/p=5.0e-5 6.04 ± 0.22 ms 6.21 ± 0.2 ms 0.972
decompress/symmetric/column/direct/n=1000/p=0.002 24.4 ± 1.3 μs 26.9 ± 1.3 μs 0.905
decompress/symmetric/column/direct/n=1000/p=0.005 0.0458 ± 0.0017 ms 0.0497 ± 0.0021 ms 0.922
decompress/symmetric/column/direct/n=1000/p=0.01 0.0831 ± 0.0033 ms 0.0884 ± 0.0039 ms 0.94
decompress/symmetric/column/direct/n=100000/p=0.0001 21.1 ± 1.8 ms 24.4 ± 0.83 ms 0.865
decompress/symmetric/column/direct/n=100000/p=2.0e-5 3.81 ± 0.37 ms 4.5 ± 0.45 ms 0.847
decompress/symmetric/column/direct/n=100000/p=5.0e-5 10.4 ± 0.38 ms 11.9 ± 0.49 ms 0.871
decompress/symmetric/column/substitution/n=1000/p=0.002 0.105 ± 0.0025 ms 0.0945 ± 0.0053 ms 1.11
decompress/symmetric/column/substitution/n=1000/p=0.005 0.195 ± 0.0075 ms 0.179 ± 0.009 ms 1.09
decompress/symmetric/column/substitution/n=1000/p=0.01 0.383 ± 0.014 ms 0.354 ± 0.011 ms 1.08
decompress/symmetric/column/substitution/n=100000/p=0.0001 0.0947 ± 0.0031 s 0.0989 ± 0.0027 s 0.957
decompress/symmetric/column/substitution/n=100000/p=2.0e-5 25 ± 0.35 ms 24.7 ± 0.22 ms 1.01
decompress/symmetric/column/substitution/n=100000/p=5.0e-5 0.0475 ± 0.00066 s 0.0501 ± 0.0007 s 0.947
time_to_load 0.219 ± 0.00088 s 0.218 ± 0.00099 s 1.01
main 6739849... main/67398491447fb4...
coloring/nonsymmetric/bidirectional/direct/n=1000/p=0.002 0.475 k allocs: 2.35 MB 0.475 k allocs: 2.35 MB 1
coloring/nonsymmetric/bidirectional/direct/n=1000/p=0.005 0.485 k allocs: 3.96 MB 0.485 k allocs: 3.96 MB 1
coloring/nonsymmetric/bidirectional/direct/n=1000/p=0.01 0.495 k allocs: 6.99 MB 0.495 k allocs: 6.99 MB 1
coloring/nonsymmetric/bidirectional/direct/n=100000/p=0.0001 0.555 k allocs: 0.712 GB 0.555 k allocs: 0.712 GB 1
coloring/nonsymmetric/bidirectional/direct/n=100000/p=2.0e-5 0.525 k allocs: 0.24 GB 0.525 k allocs: 0.24 GB 1
coloring/nonsymmetric/bidirectional/direct/n=100000/p=5.0e-5 0.545 k allocs: 0.426 GB 0.545 k allocs: 0.426 GB 1
coloring/nonsymmetric/bidirectional/substitution/n=1000/p=0.002 0.0512 M allocs: 6.36 MB 0.0449 M allocs: 5.23 MB 1.22
coloring/nonsymmetric/bidirectional/substitution/n=1000/p=0.005 0.0978 M allocs: 11.4 MB 0.0892 M allocs: 9.71 MB 1.18
coloring/nonsymmetric/bidirectional/substitution/n=1000/p=0.01 0.187 M allocs: 21.8 MB 0.172 M allocs: 18.4 MB 1.18
coloring/nonsymmetric/bidirectional/substitution/n=100000/p=0.0001 17.9 M allocs: 2.03 GB 16.6 M allocs: 1.74 GB 1.17
coloring/nonsymmetric/bidirectional/substitution/n=100000/p=2.0e-5 4.93 M allocs: 0.585 GB 4.32 M allocs: 0.498 GB 1.17
coloring/nonsymmetric/bidirectional/substitution/n=100000/p=5.0e-5 9.54 M allocs: 1.13 GB 8.74 M allocs: 0.964 GB 1.17
coloring/nonsymmetric/column/direct/n=1000/p=0.002 0.135 k allocs: 0.354 MB 0.135 k allocs: 0.354 MB 1
coloring/nonsymmetric/column/direct/n=1000/p=0.005 0.135 k allocs: 0.578 MB 0.135 k allocs: 0.578 MB 1
coloring/nonsymmetric/column/direct/n=1000/p=0.01 0.135 k allocs: 0.967 MB 0.135 k allocs: 0.967 MB 1
coloring/nonsymmetric/column/direct/n=100000/p=0.0001 0.135 k allocs: 0.0931 GB 0.135 k allocs: 0.0931 GB 1
coloring/nonsymmetric/column/direct/n=100000/p=2.0e-5 0.135 k allocs: 0.0335 GB 0.135 k allocs: 0.0335 GB 1
coloring/nonsymmetric/column/direct/n=100000/p=5.0e-5 0.135 k allocs: 0.0558 GB 0.135 k allocs: 0.0558 GB 1
coloring/nonsymmetric/row/direct/n=1000/p=0.002 0.135 k allocs: 0.354 MB 0.135 k allocs: 0.354 MB 1
coloring/nonsymmetric/row/direct/n=1000/p=0.005 0.135 k allocs: 0.578 MB 0.135 k allocs: 0.578 MB 1
coloring/nonsymmetric/row/direct/n=1000/p=0.01 0.135 k allocs: 0.967 MB 0.135 k allocs: 0.967 MB 1
coloring/nonsymmetric/row/direct/n=100000/p=0.0001 0.135 k allocs: 0.0931 GB 0.135 k allocs: 0.0931 GB 1
coloring/nonsymmetric/row/direct/n=100000/p=2.0e-5 0.135 k allocs: 0.0335 GB 0.135 k allocs: 0.0335 GB 1
coloring/nonsymmetric/row/direct/n=100000/p=5.0e-5 0.135 k allocs: 0.0558 GB 0.135 k allocs: 0.0558 GB 1
coloring/symmetric/column/direct/n=1000/p=0.002 0.22 k allocs: 0.583 MB 0.22 k allocs: 0.583 MB 1
coloring/symmetric/column/direct/n=1000/p=0.005 0.23 k allocs: 0.932 MB 0.23 k allocs: 0.932 MB 1
coloring/symmetric/column/direct/n=1000/p=0.01 0.24 k allocs: 1.57 MB 0.24 k allocs: 1.57 MB 1
coloring/symmetric/column/direct/n=100000/p=0.0001 0.3 k allocs: 0.168 GB 0.3 k allocs: 0.168 GB 1
coloring/symmetric/column/direct/n=100000/p=2.0e-5 0.27 k allocs: 0.056 GB 0.27 k allocs: 0.056 GB 1
coloring/symmetric/column/direct/n=100000/p=5.0e-5 0.29 k allocs: 0.0995 GB 0.29 k allocs: 0.0995 GB 1
coloring/symmetric/column/substitution/n=1000/p=0.002 25.5 k allocs: 2.68 MB 22.4 k allocs: 2.17 MB 1.24
coloring/symmetric/column/substitution/n=1000/p=0.005 0.0492 M allocs: 4.95 MB 0.0448 M allocs: 4.09 MB 1.21
coloring/symmetric/column/substitution/n=1000/p=0.01 0.0937 M allocs: 9.72 MB 0.0862 M allocs: 7.86 MB 1.24
coloring/symmetric/column/substitution/n=100000/p=0.0001 8.95 M allocs: 0.887 GB 8.31 M allocs: 0.74 GB 1.2
coloring/symmetric/column/substitution/n=100000/p=2.0e-5 2.47 M allocs: 0.246 GB 2.16 M allocs: 0.203 GB 1.21
coloring/symmetric/column/substitution/n=100000/p=5.0e-5 4.77 M allocs: 0.49 GB 4.37 M allocs: 0.407 GB 1.2
decompress/nonsymmetric/bidirectional/direct/n=1000/p=0.002 0.045 k allocs: 0.197 MB 0.045 k allocs: 0.197 MB 1
decompress/nonsymmetric/bidirectional/direct/n=1000/p=0.005 0.045 k allocs: 0.419 MB 0.045 k allocs: 0.419 MB 1
decompress/nonsymmetric/bidirectional/direct/n=1000/p=0.01 0.045 k allocs: 0.802 MB 0.045 k allocs: 0.802 MB 1
decompress/nonsymmetric/bidirectional/direct/n=100000/p=0.0001 0.045 k allocs: 0.0782 GB 0.045 k allocs: 0.0782 GB 1
decompress/nonsymmetric/bidirectional/direct/n=100000/p=2.0e-5 0.045 k allocs: 19.1 MB 0.045 k allocs: 19.1 MB 1
decompress/nonsymmetric/bidirectional/direct/n=100000/p=5.0e-5 0.045 k allocs: 0.0409 GB 0.045 k allocs: 0.0409 GB 1
decompress/nonsymmetric/bidirectional/substitution/n=1000/p=0.002 0.045 k allocs: 0.197 MB 0.045 k allocs: 0.197 MB 1
decompress/nonsymmetric/bidirectional/substitution/n=1000/p=0.005 0.045 k allocs: 0.419 MB 0.045 k allocs: 0.419 MB 1
decompress/nonsymmetric/bidirectional/substitution/n=1000/p=0.01 0.045 k allocs: 0.802 MB 0.045 k allocs: 0.802 MB 1
decompress/nonsymmetric/bidirectional/substitution/n=100000/p=0.0001 0.045 k allocs: 0.0782 GB 0.045 k allocs: 0.0782 GB 1
decompress/nonsymmetric/bidirectional/substitution/n=100000/p=2.0e-5 0.045 k allocs: 19.1 MB 0.045 k allocs: 19.1 MB 1
decompress/nonsymmetric/bidirectional/substitution/n=100000/p=5.0e-5 0.045 k allocs: 0.0409 GB 0.045 k allocs: 0.0409 GB 1
decompress/nonsymmetric/column/direct/n=1000/p=0.002 0.045 k allocs: 0.197 MB 0.045 k allocs: 0.197 MB 1
decompress/nonsymmetric/column/direct/n=1000/p=0.005 0.045 k allocs: 0.419 MB 0.045 k allocs: 0.419 MB 1
decompress/nonsymmetric/column/direct/n=1000/p=0.01 0.045 k allocs: 0.802 MB 0.045 k allocs: 0.802 MB 1
decompress/nonsymmetric/column/direct/n=100000/p=0.0001 0.045 k allocs: 0.0782 GB 0.045 k allocs: 0.0782 GB 1
decompress/nonsymmetric/column/direct/n=100000/p=2.0e-5 0.045 k allocs: 19.1 MB 0.045 k allocs: 19.1 MB 1
decompress/nonsymmetric/column/direct/n=100000/p=5.0e-5 0.045 k allocs: 0.0409 GB 0.045 k allocs: 0.0409 GB 1
decompress/nonsymmetric/row/direct/n=1000/p=0.002 0.045 k allocs: 0.197 MB 0.045 k allocs: 0.197 MB 1
decompress/nonsymmetric/row/direct/n=1000/p=0.005 0.045 k allocs: 0.419 MB 0.045 k allocs: 0.419 MB 1
decompress/nonsymmetric/row/direct/n=1000/p=0.01 0.045 k allocs: 0.802 MB 0.045 k allocs: 0.802 MB 1
decompress/nonsymmetric/row/direct/n=100000/p=0.0001 0.045 k allocs: 0.0782 GB 0.045 k allocs: 0.0782 GB 1
decompress/nonsymmetric/row/direct/n=100000/p=2.0e-5 0.045 k allocs: 19.1 MB 0.045 k allocs: 19.1 MB 1
decompress/nonsymmetric/row/direct/n=100000/p=5.0e-5 0.045 k allocs: 0.0409 GB 0.045 k allocs: 0.0409 GB 1
decompress/symmetric/column/direct/n=1000/p=0.002 0.045 k allocs: 0.197 MB 0.045 k allocs: 0.197 MB 1
decompress/symmetric/column/direct/n=1000/p=0.005 0.045 k allocs: 0.419 MB 0.045 k allocs: 0.419 MB 1
decompress/symmetric/column/direct/n=1000/p=0.01 0.045 k allocs: 0.802 MB 0.045 k allocs: 0.802 MB 1
decompress/symmetric/column/direct/n=100000/p=0.0001 0.045 k allocs: 0.0782 GB 0.045 k allocs: 0.0782 GB 1
decompress/symmetric/column/direct/n=100000/p=2.0e-5 0.045 k allocs: 19.1 MB 0.045 k allocs: 19.1 MB 1
decompress/symmetric/column/direct/n=100000/p=5.0e-5 0.045 k allocs: 0.0409 GB 0.045 k allocs: 0.0409 GB 1
decompress/symmetric/column/substitution/n=1000/p=0.002 0.045 k allocs: 0.197 MB 0.045 k allocs: 0.197 MB 1
decompress/symmetric/column/substitution/n=1000/p=0.005 0.045 k allocs: 0.419 MB 0.045 k allocs: 0.419 MB 1
decompress/symmetric/column/substitution/n=1000/p=0.01 0.045 k allocs: 0.802 MB 0.045 k allocs: 0.802 MB 1
decompress/symmetric/column/substitution/n=100000/p=0.0001 0.045 k allocs: 0.0782 GB 0.045 k allocs: 0.0782 GB 1
decompress/symmetric/column/substitution/n=100000/p=2.0e-5 0.045 k allocs: 19.1 MB 0.045 k allocs: 19.1 MB 1
decompress/symmetric/column/substitution/n=100000/p=5.0e-5 0.045 k allocs: 0.0409 GB 0.045 k allocs: 0.0409 GB 1
time_to_load 0.159 k allocs: 11.2 kB 0.159 k allocs: 11.2 kB 1

@amontoison amontoison removed the benchmark Run benchmarks on PR label Apr 3, 2025
gdalle
gdalle reviewed Apr 4, 2025
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I think we can use this opportunity to remove one more big alloc

src/coloring.jl

# reverse_bfs_orders contains the reverse breadth first (BFS) traversal order for each tree in the forest
for k in 1:nt
tree = trees[k]
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@gdalle gdalle Apr 4, 2025 •
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This is the only place where trees is actually used. Right now it is one dictionary per tree, which is still rather wasteful and probably accounts for a large percentage of our allocs. Can we figure out a way to get rid of this too?

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On second thought, let's do it in a separate PR, since this one works

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I started to work on it and it is not a simple task.

@gdalle gdalle merged commit ee8bb7a into main Apr 4, 2025
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@gdalle gdalle deleted the acyclic_tree branch April 4, 2025 11:22
@amontoison amontoison mentioned this pull request Apr 5, 2025
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