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Speeding up dtwf sims with large Ne #947

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ivan-krukov
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Replaced a large (Ne) array of pointers of parental segments with an AVL tree to store the offspring for each parent. This results in considerable speedups for the simulations with large Ne. Fixes #878.

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codecov bot commented Apr 7, 2020

Codecov Report

Merging #947 into master will decrease coverage by 0.02%.
The diff coverage is 87.50%.

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@@            Coverage Diff             @@
##           master     #947      +/-   ##
==========================================
- Coverage   88.05%   88.03%   -0.03%     
==========================================
  Files          16       16              
  Lines        8457     8473      +16     
  Branches     1744     1748       +4     
==========================================
+ Hits         7447     7459      +12     
- Misses        504      506       +2     
- Partials      506      508       +2     
Flag Coverage Δ
#C 88.03% <87.50%> (-0.03%) ⬇️
#python 98.14% <ø> (ø)
Impacted Files Coverage Δ
lib/msprime.c 84.12% <87.50%> (-0.05%) ⬇️

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@jeromekelleher
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Sorry @ivan-krukov, this seems to have slipped under the radar somehow. Would it be possible to bring this up to date please? We have some benchmarks now, so it should be easy to quantify the improvements.

@benjeffery benjeffery changed the base branch from master to main September 28, 2020 12:09
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@ivan-krukov do you think we can bring this up to date and get ready for merging? The merge window for msprime 1.0 is quickly approaching, and we'd need to have this sorted out in the next week if it's going to get in for the release. It would be a shame for it to miss out, since it's a significant perf improvement.

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Closing this as it's a long way behind the head of main. It would be nice to incorporate this idea back into the DTWF simulation at some point, as it should have a significant impact.

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[C code] DTWF performance
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