Decompression of acyclic coloring with SparseMatrixCSC

[amontoison]

close #93

• Add the following method:

decompress!(A::SparseMatrixCSC{R}, B::AbstractMatrix{R}, result::TreeSetColoringResult, uplo::Symbol=:F)
   ...
end

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (7146a7d) to head (9c35c8a).
Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff            @@
##              main      #130   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           12        12           
  Lines          884       960   +76     
=========================================
+ Hits           884       960   +76     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[github-actions]

Benchmark Results

	main	9c35c8a...	main/9c35c8aa19b9c7...
coloring/nonsymmetric/column/direct/n=1000/p=0.002	0.0882 ± 0.0038 ms	0.0882 ± 0.0037 ms	1
coloring/nonsymmetric/column/direct/n=1000/p=0.005	0.188 ± 0.0068 ms	0.19 ± 0.0064 ms	0.994
coloring/nonsymmetric/column/direct/n=1000/p=0.01	0.387 ± 0.013 ms	0.391 ± 0.012 ms	0.989
coloring/nonsymmetric/column/direct/n=100000/p=0.0001	0.069 ± 0.0034 s	0.0675 ± 0.0025 s	1.02
coloring/nonsymmetric/column/direct/n=100000/p=2.0e-5	12.7 ± 0.47 ms	12.9 ± 0.54 ms	0.986
coloring/nonsymmetric/column/direct/n=100000/p=5.0e-5	31.6 ± 1.2 ms	31.2 ± 0.94 ms	1.01
coloring/nonsymmetric/row/direct/n=1000/p=0.002	0.0864 ± 0.0036 ms	0.0865 ± 0.0035 ms	0.999
coloring/nonsymmetric/row/direct/n=1000/p=0.005	0.187 ± 0.0074 ms	0.187 ± 0.0064 ms	1
coloring/nonsymmetric/row/direct/n=1000/p=0.01	0.388 ± 0.013 ms	0.386 ± 0.013 ms	1.01
coloring/nonsymmetric/row/direct/n=100000/p=0.0001	0.0702 ± 0.0033 s	0.0704 ± 0.003 s	0.997
coloring/nonsymmetric/row/direct/n=100000/p=2.0e-5	12.7 ± 0.64 ms	12.7 ± 0.55 ms	1
coloring/nonsymmetric/row/direct/n=100000/p=5.0e-5	31.4 ± 1.4 ms	31.1 ± 1.2 ms	1.01
coloring/symmetric/column/direct/n=1000/p=0.002	0.25 ± 0.012 ms	0.252 ± 0.012 ms	0.994
coloring/symmetric/column/direct/n=1000/p=0.005	0.677 ± 0.028 ms	0.679 ± 0.028 ms	0.996
coloring/symmetric/column/direct/n=1000/p=0.01	1.63 ± 0.066 ms	1.64 ± 0.07 ms	0.993
coloring/symmetric/column/direct/n=100000/p=0.0001	0.404 ± 0.03 s	0.369 ± 0.057 s	1.1
coloring/symmetric/column/direct/n=100000/p=2.0e-5	0.0342 ± 0.0017 s	0.0341 ± 0.0018 s	1
coloring/symmetric/column/direct/n=100000/p=5.0e-5	0.121 ± 0.015 s	0.118 ± 0.0076 s	1.03
coloring/symmetric/column/substitution/n=1000/p=0.002	0.576 ± 0.031 ms	0.628 ± 0.034 ms	0.918
coloring/symmetric/column/substitution/n=1000/p=0.005	1.56 ± 0.078 ms	1.68 ± 0.083 ms	0.925
coloring/symmetric/column/substitution/n=1000/p=0.01	3.31 ± 0.14 ms	3.57 ± 0.12 ms	0.927
coloring/symmetric/column/substitution/n=100000/p=0.0001	0.808 ± 0.045 s	0.855 ± 0.035 s	0.945
coloring/symmetric/column/substitution/n=100000/p=2.0e-5	0.0966 ± 0.0099 s	0.0998 ± 0.01 s	0.968
coloring/symmetric/column/substitution/n=100000/p=5.0e-5	0.304 ± 0.02 s	0.315 ± 0.025 s	0.965
decompress/nonsymmetric/column/direct/n=1000/p=0.002	4.72 ± 0.57 μs	4.28 ± 0.49 μs	1.1
decompress/nonsymmetric/column/direct/n=1000/p=0.005	8.09 ± 1.1 μs	7.66 ± 0.84 μs	1.06
decompress/nonsymmetric/column/direct/n=1000/p=0.01	24.6 ± 6.9 μs	22.8 ± 6.8 μs	1.08
decompress/nonsymmetric/column/direct/n=100000/p=0.0001	5.12 ± 0.4 ms	5.32 ± 0.36 ms	0.963
decompress/nonsymmetric/column/direct/n=100000/p=2.0e-5	0.992 ± 0.18 ms	1.04 ± 0.11 ms	0.956
decompress/nonsymmetric/column/direct/n=100000/p=5.0e-5	2.52 ± 0.7 ms	2.63 ± 0.55 ms	0.958
decompress/nonsymmetric/row/direct/n=1000/p=0.002	5.23 ± 0.56 μs	4.46 ± 0.5 μs	1.17
decompress/nonsymmetric/row/direct/n=1000/p=0.005	8.22 ± 0.79 μs	7.24 ± 0.59 μs	1.14
decompress/nonsymmetric/row/direct/n=1000/p=0.01	17 ± 3.5 μs	16.1 ± 2.6 μs	1.06
decompress/nonsymmetric/row/direct/n=100000/p=0.0001	2.02 ± 0.3 ms	2.03 ± 0.41 ms	0.998
decompress/nonsymmetric/row/direct/n=100000/p=2.0e-5	0.445 ± 0.28 ms	0.402 ± 0.069 ms	1.11
decompress/nonsymmetric/row/direct/n=100000/p=5.0e-5	1.04 ± 0.79 ms	0.959 ± 0.54 ms	1.08
decompress/symmetric/column/direct/n=1000/p=0.002	5.4 ± 0.68 μs	4.73 ± 0.61 μs	1.14
decompress/symmetric/column/direct/n=1000/p=0.005	8.07 ± 0.84 μs	7.69 ± 0.77 μs	1.05
decompress/symmetric/column/direct/n=1000/p=0.01	22.3 ± 4.6 μs	21.7 ± 5.1 μs	1.03
decompress/symmetric/column/direct/n=100000/p=0.0001	4.9 ± 0.19 ms	4.87 ± 0.19 ms	1.01
decompress/symmetric/column/direct/n=100000/p=2.0e-5	0.972 ± 0.13 ms	0.93 ± 0.079 ms	1.04
decompress/symmetric/column/direct/n=100000/p=5.0e-5	2.42 ± 0.087 ms	2.37 ± 0.2 ms	1.02
decompress/symmetric/column/substitution/n=1000/p=0.002	0.07 ± 0.0035 ms	21.8 ± 2.4 μs	3.21
decompress/symmetric/column/substitution/n=1000/p=0.005	0.171 ± 0.0074 ms	0.0393 ± 0.002 ms	4.35
decompress/symmetric/column/substitution/n=1000/p=0.01	0.353 ± 0.011 ms	0.0749 ± 0.0034 ms	4.71
decompress/symmetric/column/substitution/n=100000/p=0.0001	0.074 ± 0.01 s	20.3 ± 2.6 ms	3.64
decompress/symmetric/column/substitution/n=100000/p=2.0e-5	13 ± 1.1 ms	5.63 ± 0.4 ms	2.31
decompress/symmetric/column/substitution/n=100000/p=5.0e-5	0.0327 ± 0.0023 s	10.9 ± 1.8 ms	3
time_to_load	0.269 ± 0.0012 s	0.268 ± 0.0011 s	1

	main	9c35c8a...	main/9c35c8aa19b9c7...
coloring/nonsymmetric/column/direct/n=1000/p=0.002	24 allocs: 0.0588 MB	24 allocs: 0.0587 MB	1
coloring/nonsymmetric/column/direct/n=1000/p=0.005	24 allocs: 0.102 MB	24 allocs: 0.103 MB	0.997
coloring/nonsymmetric/column/direct/n=1000/p=0.01	24 allocs: 0.176 MB	24 allocs: 0.178 MB	0.994
coloring/nonsymmetric/column/direct/n=100000/p=0.0001	24 allocs: 18.3 MB	24 allocs: 18.3 MB	0.999
coloring/nonsymmetric/column/direct/n=100000/p=2.0e-5	24 allocs: 6.07 MB	24 allocs: 6.08 MB	0.998
coloring/nonsymmetric/column/direct/n=100000/p=5.0e-5	24 allocs: 10.6 MB	24 allocs: 10.6 MB	1
coloring/nonsymmetric/row/direct/n=1000/p=0.002	24 allocs: 0.0586 MB	24 allocs: 0.0582 MB	1.01
coloring/nonsymmetric/row/direct/n=1000/p=0.005	24 allocs: 0.103 MB	24 allocs: 0.103 MB	1
coloring/nonsymmetric/row/direct/n=1000/p=0.01	24 allocs: 0.178 MB	24 allocs: 0.177 MB	1
coloring/nonsymmetric/row/direct/n=100000/p=0.0001	24 allocs: 18.3 MB	24 allocs: 18.3 MB	1
coloring/nonsymmetric/row/direct/n=100000/p=2.0e-5	24 allocs: 6.07 MB	24 allocs: 6.08 MB	0.999
coloring/nonsymmetric/row/direct/n=100000/p=5.0e-5	24 allocs: 10.6 MB	24 allocs: 10.6 MB	1
coloring/symmetric/column/direct/n=1000/p=0.002	1.08 k allocs: 0.265 MB	1.09 k allocs: 0.266 MB	0.998
coloring/symmetric/column/direct/n=1000/p=0.005	2.65 k allocs: 0.403 MB	2.71 k allocs: 0.407 MB	0.99
coloring/symmetric/column/direct/n=1000/p=0.01	5.74 k allocs: 1.06 MB	5.75 k allocs: 1.06 MB	1
coloring/symmetric/column/direct/n=100000/p=0.0001	0.604 M allocs: 0.103 GB	0.602 M allocs: 0.103 GB	1
coloring/symmetric/column/direct/n=100000/p=2.0e-5	0.117 M allocs: 22.8 MB	0.117 M allocs: 22.8 MB	1
coloring/symmetric/column/direct/n=100000/p=5.0e-5	0.287 M allocs: 0.0506 GB	0.287 M allocs: 0.0506 GB	1
coloring/symmetric/column/substitution/n=1000/p=0.002	4.96 k allocs: 0.645 MB	4.89 k allocs: 0.66 MB	0.976
coloring/symmetric/column/substitution/n=1000/p=0.005	9.78 k allocs: 1.17 MB	9.71 k allocs: 1.21 MB	0.967
coloring/symmetric/column/substitution/n=1000/p=0.01	19 k allocs: 2.63 MB	18.9 k allocs: 2.69 MB	0.976
coloring/symmetric/column/substitution/n=100000/p=0.0001	1.91 M allocs: 0.241 GB	1.91 M allocs: 0.25 GB	0.964
coloring/symmetric/column/substitution/n=100000/p=2.0e-5	0.549 M allocs: 0.0607 GB	0.55 M allocs: 0.0623 GB	0.975
coloring/symmetric/column/substitution/n=100000/p=5.0e-5	1.03 M allocs: 0.125 GB	1.03 M allocs: 0.129 GB	0.967
decompress/nonsymmetric/column/direct/n=1000/p=0.002	9 allocs: 0.035 MB	9 allocs: 0.0342 MB	1.02
decompress/nonsymmetric/column/direct/n=1000/p=0.005	9 allocs: 0.0786 MB	9 allocs: 0.0786 MB	1
decompress/nonsymmetric/column/direct/n=1000/p=0.01	9 allocs: 0.153 MB	9 allocs: 0.153 MB	1
decompress/nonsymmetric/column/direct/n=100000/p=0.0001	9 allocs: 16 MB	9 allocs: 16 MB	1
decompress/nonsymmetric/column/direct/n=100000/p=2.0e-5	9 allocs: 3.78 MB	9 allocs: 3.79 MB	0.996
decompress/nonsymmetric/column/direct/n=100000/p=5.0e-5	9 allocs: 8.35 MB	9 allocs: 8.36 MB	0.999
decompress/nonsymmetric/row/direct/n=1000/p=0.002	9 allocs: 0.0347 MB	9 allocs: 0.0352 MB	0.986
decompress/nonsymmetric/row/direct/n=1000/p=0.005	9 allocs: 0.0792 MB	9 allocs: 0.0794 MB	0.997
decompress/nonsymmetric/row/direct/n=1000/p=0.01	9 allocs: 0.154 MB	9 allocs: 0.155 MB	0.991
decompress/nonsymmetric/row/direct/n=100000/p=0.0001	9 allocs: 16 MB	9 allocs: 16 MB	1
decompress/nonsymmetric/row/direct/n=100000/p=2.0e-5	9 allocs: 3.79 MB	9 allocs: 3.79 MB	1
decompress/nonsymmetric/row/direct/n=100000/p=5.0e-5	9 allocs: 8.36 MB	9 allocs: 8.34 MB	1
decompress/symmetric/column/direct/n=1000/p=0.002	9 allocs: 0.0347 MB	9 allocs: 0.0347 MB	1
decompress/symmetric/column/direct/n=1000/p=0.005	9 allocs: 0.0788 MB	9 allocs: 0.0784 MB	1
decompress/symmetric/column/direct/n=1000/p=0.01	9 allocs: 0.152 MB	9 allocs: 0.153 MB	0.994
decompress/symmetric/column/direct/n=100000/p=0.0001	9 allocs: 16 MB	9 allocs: 16 MB	0.999
decompress/symmetric/column/direct/n=100000/p=2.0e-5	9 allocs: 3.79 MB	9 allocs: 3.79 MB	0.999
decompress/symmetric/column/direct/n=100000/p=5.0e-5	9 allocs: 8.37 MB	9 allocs: 8.37 MB	1
decompress/symmetric/column/substitution/n=1000/p=0.002	9 allocs: 0.035 MB	9 allocs: 0.0351 MB	0.997
decompress/symmetric/column/substitution/n=1000/p=0.005	9 allocs: 0.0787 MB	9 allocs: 0.0789 MB	0.997
decompress/symmetric/column/substitution/n=1000/p=0.01	9 allocs: 0.153 MB	9 allocs: 0.154 MB	0.994
decompress/symmetric/column/substitution/n=100000/p=0.0001	9 allocs: 16 MB	9 allocs: 16 MB	1
decompress/symmetric/column/substitution/n=100000/p=2.0e-5	9 allocs: 3.79 MB	9 allocs: 3.8 MB	0.997
decompress/symmetric/column/substitution/n=100000/p=5.0e-5	9 allocs: 8.39 MB	9 allocs: 8.36 MB	1
time_to_load	0.157 k allocs: 11.1 kB	0.157 k allocs: 11.1 kB	1

[amontoison]

@gdalle I spend a few hours to implement an optimized version and it's 2-4x time slower 💀

[gdalle]

I think you're reading the benchmarks wrong? The last column is main over your branch, so your method is actually faster?

[amontoison]

Yep, you are right. I don't know how to read the benchmarks. 🤪
In ADNLPModels.jl, we have an improvement if the ratio is less than 1. The ratio is inverted here.
The results are quite good!

[amontoison]

@gdalle Can you review this PR if you find time?

[gdalle]

Sure, I'll do it tomorrow