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DirectCR-RSSA #346

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Vilin97
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@Vilin97 Vilin97 commented Sep 11, 2023 •
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A new spatial SSA called DirectCRRSSA uses RSSA-style sampling to sample the site+jump. It is about 20% faster than DirectCRDirect, at least on the problem in the test/spatial/ABC.jl (5 sites in a line, 3 species, 2 reactions).

using BenchmarkTools
@btime solve(jump_problems[1], SSAStepper()) # NSM with a `CartesianGrid`, 52ms
@btime solve(jump_problems[2], SSAStepper()) # NSM with a `Graph`, 49ms
@btime solve(jump_problems[3], SSAStepper()) # DirectCRDirect with  a `CartesianGrid`, 51ms
@btime solve(jump_problems[4], SSAStepper()) # DirectCRRSSA with a `CartesianGrid`, 42ms

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Pull Request Test Coverage Report for Build 6141985002

  • 172 of 181 (95.03%) changed or added relevant lines in 8 files are covered.
  • 12 unchanged lines in 5 files lost coverage.
  • Overall coverage decreased (-0.1%) to 89.759%
Changes Missing Coverage Covered Lines Changed/Added Lines %
src/spatial/bracketing.jl 35 38 92.11%
src/spatial/rssacrdirect.jl 105 111 94.59%
Files with Coverage Reduction New Missed Lines %
src/aggregators/prioritytable.jl 1 86.86%
src/extended_jump_array.jl 1 80.52%
src/coupling.jl 2 78.18%
src/spatial/spatial_massaction_jump.jl 3 85.45%
src/spatial/directcrdirect.jl 5 87.65%
Totals Coverage Status
Change from base Build 6133295964: -0.1%
Covered Lines: 2419
Relevant Lines: 2695
💛 - Coveralls

Vilin97
Vilin97 commented Sep 12, 2023
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src/spatial/hop_rates.jl
spatial_system)
@inbounds for spec in species
update_hop_rate!(hop_rates, spec, u, site, spatial_system)
function update_hop_rates!(hop_rates::AbstractHopRates, species_vec, u, site, spatial_system)
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If species_vec is a single species, the function reduces to updating a single hop rate. So I deleted update_hop_rate!.

@Vilin97 Vilin97 marked this pull request as ready for review September 12, 2023 01:29
@Vilin97 Vilin97 changed the title [WIP] CR-RSSA DirectCR-RSSA Sep 12, 2023
Vilin97
Vilin97 commented Sep 12, 2023
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src/spatial/directcrdirect.jl Outdated
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There was a very hard-to-find bug in the ordering of arguments in generate_jumps!. I fixed it here and in NSM.jl.

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coveralls commented Sep 12, 2023 •
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Pull Request Test Coverage Report for Build 6180696485

  • 155 of 161 (96.27%) changed or added relevant lines in 8 files are covered.
  • No unchanged relevant lines lost coverage.
  • Overall coverage increased (+0.3%) to 90.175%
Changes Missing Coverage Covered Lines Changed/Added Lines %
src/spatial/bracketing.jl 23 24 95.83%
src/spatial/directcrrssa.jl 106 111 95.5%
Totals Coverage Status
Change from base Build 6167199515: 0.3%
Covered Lines: 2423
Relevant Lines: 2687
💛 - Coveralls

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