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Replace cumsum broadcast with accumulate #472

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seabbs
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@seabbs seabbs commented Oct 4, 2024

Tests a single change from #470

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github-actions bot commented Oct 4, 2024

Try this Pull Request!

Open Julia and type:

import Pkg
Pkg.activate(temp=true)
Pkg.add(url="https://github.com/CDCgov/Rt-without-renewal", rev="accumulate-vs-cumsum-broadcast", subdir="EpiAware")
using EpiAware

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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 90.02%. Comparing base (21fb991) to head (86af1a7).

Additional details and impacted files 
@@           Coverage Diff           @@
##             main     #472   +/-   ##
=======================================
  Coverage   90.02%   90.02%           
=======================================
  Files          57       57           
  Lines         742      742           
=======================================
  Hits          668      668           
  Misses         74       74

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

@SamuelBrand1 SamuelBrand1 mentioned this pull request Oct 4, 2024
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Benchmark result

Judge result

Benchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewal

Job Properties

  • Time of benchmarks:
    • Target: 4 Oct 2024 - 11:24
    • Baseline: 4 Oct 2024 - 11:48
  • Package commits:
    • Target: 346dd5
    • Baseline: 21fb99
  • Julia commits:
    • Target: 6f3fdf
    • Baseline: 6f3fdf
  • Julia command flags:
    • Target: None
    • Baseline: None
  • Environment variables:
    • Target: None
    • Baseline: None

Results

A ratio greater than 1.0 denotes a possible regression (marked with ❌), while a ratio less
than 1.0 denotes a possible improvement (marked with ✅). Only significant results - results
that indicate possible regressions or improvements - are shown below (thus, an empty table means that all
benchmark results remained invariant between builds).

ID time ratio memory ratio
["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 1.07 (5%) ❌ 1.00 (1%)
["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 1.06 (5%) ❌ 1.00 (1%)
["EpiInfModels", "ExpGrowthRate", "evaluation", "linked"] 1.13 (5%) ❌ 1.06 (1%) ❌
["EpiInfModels", "ExpGrowthRate", "evaluation", "standard"] 1.12 (5%) ❌ 1.06 (1%) ❌
["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 1.10 (5%) ❌ 1.12 (1%) ❌
["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.11 (5%) ❌ 1.12 (1%) ❌
["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 0.40 (5%) ✅ 0.70 (1%) ✅
["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 0.40 (5%) ✅ 0.70 (1%) ✅
["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 1.02 (5%) 0.35 (1%) ✅
["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 1.03 (5%) 0.35 (1%) ✅
["EpiLatentModels", "BroadcastLatentModel", "evaluation", "standard"] 1.07 (5%) ❌ 1.00 (1%)
["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 1.06 (5%) ❌ 1.00 (1%)
["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.08 (5%) ❌ 1.00 (1%)
["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 1.08 (5%) ❌ 1.00 (1%)
["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 1.06 (5%) ❌ 1.00 (1%)
["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 1.45 (5%) ❌ 1.00 (1%)
["EpiLatentModels", "Intercept", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 1.06 (5%) ❌ 1.00 (1%)
["EpiLatentModels", "PrefixLatentModel", "evaluation", "standard"] 0.94 (5%) ✅ 1.00 (1%)
["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 1.25 (5%) ❌ 1.00 (1%)
["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.07 (5%) ❌ 1.00 (1%)
["EpiLatentModels", "RandomWalk", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 1.05 (5%) ❌ 1.00 (1%)
["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 1.07 (5%) ❌ 1.00 (1%)
["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.08 (5%) ❌ 1.00 (1%)
["EpiLatentModels", "TransformLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 1.06 (5%) ❌ 1.00 (1%)
["EpiLatentModels", "broadcast_dayofweek", "evaluation", "linked"] 1.05 (5%) ❌ 1.00 (1%)
["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 1.05 (5%) ❌ 1.00 (1%)
["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.08 (5%) ❌ 1.00 (1%)
["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.14 (5%) ❌ 1.00 (1%)
["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 1.06 (5%) ❌ 1.00 (1%)
["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 1.06 (5%) ❌ 1.00 (1%)
["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.07 (5%) ❌ 1.00 (1%)
["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 0.95 (5%) ✅ 1.00 (1%)
["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 0.93 (5%) ✅ 1.00 (1%)
["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 1.12 (5%) ❌ 1.00 (1%)
["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.14 (5%) ❌ 1.00 (1%)
["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 1.15 (5%) ❌ 1.00 (1%)
["EpiObsModels", "PrefixObservationModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 1.07 (5%) ❌ 1.00 (1%)
["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.07 (5%) ❌ 1.00 (1%)
["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 0.95 (5%) ✅ 1.00 (1%)
["EpiObsModels", "observation_error", "no missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 1.12 (5%) ❌ 1.00 (1%)
["EpiObsModels", "observation_error", "no missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.12 (5%) ❌ 1.00 (1%)
["EpiObsModels", "observation_error", "no missing obs", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 1.06 (5%) ❌ 1.00 (1%)

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

  • ["EpiAwareUtils"]
  • ["EpiInfModels", "DirectInfections", "evaluation"]
  • ["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiInfModels", "ExpGrowthRate", "evaluation"]
  • ["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "AR", "evaluation"]
  • ["EpiLatentModels", "AR", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "AR", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "AR", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "BroadcastLatentModel", "evaluation"]
  • ["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "CombineLatentModels", "evaluation"]
  • ["EpiLatentModels", "CombineLatentModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "CombineLatentModels", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "CombineLatentModels", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "ConcatLatentModels", "evaluation"]
  • ["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "DiffLatentModel", "evaluation"]
  • ["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "HierarchicalNormal", "evaluation"]
  • ["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "Intercept", "evaluation"]
  • ["EpiLatentModels", "Intercept", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "Intercept", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "Intercept", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "PrefixLatentModel", "evaluation"]
  • ["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "RandomWalk", "evaluation"]
  • ["EpiLatentModels", "RandomWalk", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "RandomWalk", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "RandomWalk", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "RecordExpectedLatent", "evaluation"]
  • ["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "TransformLatentModel", "evaluation"]
  • ["EpiLatentModels", "TransformLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "TransformLatentModel", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "TransformLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "broadcast_dayofweek", "evaluation"]
  • ["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "broadcast_weekly", "evaluation"]
  • ["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "Ascertainment", "evaluation"]
  • ["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "LatentDelay", "evaluation"]
  • ["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "NegativeBinomialError", "evaluation"]
  • ["EpiObsModels", "NegativeBinomialError", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "NegativeBinomialError", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "NegativeBinomialError", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "PoissonError", "evaluation"]
  • ["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "PrefixObservationModel", "evaluation"]
  • ["EpiObsModels", "PrefixObservationModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "PrefixObservationModel", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "PrefixObservationModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "StackObservationModels", "evaluation"]
  • ["EpiObsModels", "StackObservationModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "StackObservationModels", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "StackObservationModels", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "ascertainment_dayofweek", "evaluation"]
  • ["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "observation_error", "missing obs", "evaluation"]
  • ["EpiObsModels", "observation_error", "missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "observation_error", "missing obs", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "observation_error", "missing obs", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "observation_error", "no missing obs", "evaluation"]
  • ["EpiObsModels", "observation_error", "no missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "observation_error", "no missing obs", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "observation_error", "no missing obs", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "observation_error", "partially missing obs", "evaluation"]
  • ["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]

Julia versioninfo

Target

Julia Version 1.10.5
Commit 6f3fdf7b362 (2024-08-27 14:19 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.5 LTS
  uname: Linux 6.8.0-1014-azure #16~22.04.1-Ubuntu SMP Thu Aug 15 21:31:41 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3003 MHz       5338 s          0 s        571 s      12185 s          0 s
       #2  3240 MHz       5433 s          0 s        604 s      12052 s          0 s
       #3  3016 MHz       4444 s          0 s        504 s      13146 s          0 s
       #4  2606 MHz       5215 s          0 s        473 s      12409 s          0 s
  Memory: 15.615272521972656 GB (12372.41796875 MB free)
  Uptime: 1813.95 sec
  Load Avg:  1.0  1.0  1.0
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Baseline

Julia Version 1.10.5
Commit 6f3fdf7b362 (2024-08-27 14:19 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.5 LTS
  uname: Linux 6.8.0-1014-azure #16~22.04.1-Ubuntu SMP Thu Aug 15 21:31:41 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2445 MHz       7958 s          0 s        910 s      23623 s          0 s
       #2  3243 MHz       8018 s          0 s        955 s      23514 s          0 s
       #3  3236 MHz       7442 s          0 s        868 s      24186 s          0 s
       #4  3184 MHz      10452 s          0 s        906 s      21144 s          0 s
  Memory: 15.615272521972656 GB (12376.49609375 MB free)
  Uptime: 3255.83 sec
  Load Avg:  1.02  1.04  1.0
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Target result

Benchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewal

Job Properties

  • Time of benchmark: 4 Oct 2024 - 11:24
  • Package commit: 346dd5
  • Julia commit: 6f3fdf
  • Julia command flags: None
  • Environment variables: None

Results

Below is a table of this job's results, obtained by running the benchmarks.
The values listed in the ID column have the structure [parent_group, child_group, ..., key], and can be used to
index into the BaseBenchmarks suite to retrieve the corresponding benchmarks.
The percentages accompanying time and memory values in the below table are noise tolerances. The "true"
time/memory value for a given benchmark is expected to fall within this percentage of the reported value.
An empty cell means that the value was zero.

ID time GC time memory allocations
["EpiAwareUtils", "censored_pmf"] 2.045 μs (5%) 416 bytes (1%) 5
["EpiInfModels", "DirectInfections", "evaluation", "linked"] 293.351 ns (5%) 432 bytes (1%) 7
["EpiInfModels", "DirectInfections", "evaluation", "standard"] 296.000 ns (5%) 432 bytes (1%) 7
["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 440.673 ns (5%) 784 bytes (1%) 13
["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 443.844 ns (5%) 784 bytes (1%) 13
["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 9.779 μs (5%) 5.62 KiB (1%) 115
["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 9.798 μs (5%) 5.62 KiB (1%) 115
["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 570.353 ns (5%) 272 bytes (1%) 6
["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 579.154 ns (5%) 272 bytes (1%) 6
["EpiInfModels", "ExpGrowthRate", "evaluation", "linked"] 238.601 ns (5%) 272 bytes (1%) 5
["EpiInfModels", "ExpGrowthRate", "evaluation", "standard"] 235.392 ns (5%) 272 bytes (1%) 5
["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 339.076 ns (5%) 576 bytes (1%) 10
["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 338.449 ns (5%) 576 bytes (1%) 10
["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 3.658 μs (5%) 3.92 KiB (1%) 92
["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 3.648 μs (5%) 3.92 KiB (1%) 92
["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 563.163 ns (5%) 96 bytes (1%) 2
["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 560.286 ns (5%) 96 bytes (1%) 2
["EpiLatentModels", "AR", "evaluation", "linked"] 2.103 μs (5%) 3.84 KiB (1%) 45
["EpiLatentModels", "AR", "evaluation", "standard"] 1.656 μs (5%) 2.80 KiB (1%) 38
["EpiLatentModels", "AR", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 3.420 μs (5%) 11.69 KiB (1%) 55
["EpiLatentModels", "AR", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 2.950 μs (5%) 10.12 KiB (1%) 46
["EpiLatentModels", "AR", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 105.807 μs (5%) 55.31 KiB (1%) 1113
["EpiLatentModels", "AR", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 70.010 μs (5%) 40.64 KiB (1%) 818
["EpiLatentModels", "AR", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 17.653 μs (5%) 8.44 KiB (1%) 225
["EpiLatentModels", "AR", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 15.820 μs (5%) 7.31 KiB (1%) 207
["EpiLatentModels", "BroadcastLatentModel", "evaluation", "linked"] 1.564 μs (5%) 3.05 KiB (1%) 34
["EpiLatentModels", "BroadcastLatentModel", "evaluation", "standard"] 1.337 μs (5%) 2.17 KiB (1%) 30
["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 2.057 μs (5%) 5.16 KiB (1%) 41
["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.791 μs (5%) 4.28 KiB (1%) 37
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["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 28.222 μs (5%) 16.86 KiB (1%) 333
["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 3.022 μs (5%) 1.00 KiB (1%) 27
["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 2.775 μs (5%) 1.00 KiB (1%) 27
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["EpiLatentModels", "CombineLatentModels", "evaluation", "standard"] 59.510 μs (5%) 37.69 KiB (1%) 536
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["EpiLatentModels", "CombineLatentModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 122.176 μs (5%) 89.31 KiB (1%) 1092
["EpiLatentModels", "CombineLatentModels", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 191.526 μs (5%) 107.81 KiB (1%) 1710
["EpiLatentModels", "CombineLatentModels", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 148.806 μs (5%) 79.61 KiB (1%) 1378
["EpiLatentModels", "CombineLatentModels", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 18.084 μs (5%) 8.58 KiB (1%) 226
["EpiLatentModels", "CombineLatentModels", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 16.390 μs (5%) 7.45 KiB (1%) 208
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["EpiLatentModels", "ConcatLatentModels", "evaluation", "standard"] 9.007 μs (5%) 21.95 KiB (1%) 184
["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 13.936 μs (5%) 34.09 KiB (1%) 224
["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 10.339 μs (5%) 25.66 KiB (1%) 194
["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 73.226 μs (5%) 56.38 KiB (1%) 719
["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 52.939 μs (5%) 42.72 KiB (1%) 580
["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 5.399 μs (5%) 2.19 KiB (1%) 52
["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 5.088 μs (5%) 2.19 KiB (1%) 52
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["EpiLatentModels", "DiffLatentModel", "evaluation", "standard"] 1.345 μs (5%) 2.48 KiB (1%) 31
["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 2.741 μs (5%) 12.62 KiB (1%) 45
["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 2.437 μs (5%) 10.94 KiB (1%) 39
["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 59.150 μs (5%) 38.81 KiB (1%) 748
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["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 6.921 μs (5%) 2.22 KiB (1%) 51
["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 6.823 μs (5%) 2.22 KiB (1%) 51
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["EpiLatentModels", "HierarchicalNormal", "evaluation", "standard"] 356.033 ns (5%) 864 bytes (1%) 7
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["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 901.700 ns (5%) 5.12 KiB (1%) 13
["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 41.397 μs (5%) 19.83 KiB (1%) 376
["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 26.279 μs (5%) 14.45 KiB (1%) 266
["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 1.269 μs (5%) 656 bytes (1%) 11
["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 1.071 μs (5%) 656 bytes (1%) 11
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["EpiLatentModels", "Intercept", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 4.298 μs (5%) 3.53 KiB (1%) 76
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["EpiLatentModels", "Intercept", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 475.781 ns (5%) 240 bytes (1%) 3
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["EpiLatentModels", "PrefixLatentModel", "evaluation", "standard"] 1.618 μs (5%) 3.00 KiB (1%) 27
["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 3.119 μs (5%) 7.75 KiB (1%) 36
["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 2.312 μs (5%) 7.28 KiB (1%) 33
["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 44.623 μs (5%) 22.16 KiB (1%) 397
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["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 1.062 μs (5%) 656 bytes (1%) 11
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["EpiLatentModels", "RandomWalk", "evaluation", "standard"] 764.516 ns (5%) 1.42 KiB (1%) 16
["EpiLatentModels", "RandomWalk", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 1.657 μs (5%) 8.73 KiB (1%) 25
["EpiLatentModels", "RandomWalk", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.672 μs (5%) 8.30 KiB (1%) 23
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["EpiLatentModels", "RandomWalk", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 3.429 μs (5%) 1.31 KiB (1%) 27
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["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 726.156 ns (5%) 1.41 KiB (1%) 16
["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 41.347 μs (5%) 19.08 KiB (1%) 380
["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 25.898 μs (5%) 13.55 KiB (1%) 269
["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 1.163 μs (5%) 400 bytes (1%) 11
["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 971.800 ns (5%) 400 bytes (1%) 11
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["EpiLatentModels", "TransformLatentModel", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 4.530 μs (5%) 3.84 KiB (1%) 81
["EpiLatentModels", "TransformLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 552.738 ns (5%) 192 bytes (1%) 3
["EpiLatentModels", "TransformLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 551.829 ns (5%) 192 bytes (1%) 3
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["EpiLatentModels", "broadcast_dayofweek", "evaluation", "standard"] 1.616 μs (5%) 2.84 KiB (1%) 38
["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 2.847 μs (5%) 10.00 KiB (1%) 51
["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 2.575 μs (5%) 8.69 KiB (1%) 45
["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 58.419 μs (5%) 35.58 KiB (1%) 689
["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 41.427 μs (5%) 29.05 KiB (1%) 574
["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 5.316 μs (5%) 1.22 KiB (1%) 27
["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 5.068 μs (5%) 1.22 KiB (1%) 27
["EpiLatentModels", "broadcast_weekly", "evaluation", "linked"] 2.192 μs (5%) 4.52 KiB (1%) 47
["EpiLatentModels", "broadcast_weekly", "evaluation", "standard"] 1.681 μs (5%) 2.62 KiB (1%) 37
["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 2.885 μs (5%) 7.69 KiB (1%) 57
["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 2.542 μs (5%) 5.53 KiB (1%) 45
["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 83.875 μs (5%) 41.95 KiB (1%) 771
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["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 5.465 μs (5%) 1.81 KiB (1%) 49
["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 4.749 μs (5%) 1.69 KiB (1%) 47
["EpiObsModels", "Ascertainment", "evaluation", "linked"] 3.262 μs (5%) 3.42 KiB (1%) 49
["EpiObsModels", "Ascertainment", "evaluation", "standard"] 3.230 μs (5%) 3.42 KiB (1%) 49
["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 4.361 μs (5%) 3.77 KiB (1%) 56
["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 4.256 μs (5%) 3.77 KiB (1%) 56
["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 49.041 μs (5%) 39.05 KiB (1%) 905
["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 33.362 μs (5%) 33.83 KiB (1%) 796
["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 5.829 μs (5%) 96 bytes (1%) 2
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["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 23.213 μs (5%) 22.36 KiB (1%) 211
["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 22.692 μs (5%) 22.36 KiB (1%) 211
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["EpiObsModels", "NegativeBinomialError", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 1.761 μs (5%) 560 bytes (1%) 10
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["EpiObsModels", "NegativeBinomialError", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 46.025 μs (5%) 36.33 KiB (1%) 899
["EpiObsModels", "NegativeBinomialError", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 31.419 μs (5%) 31.11 KiB (1%) 790
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["EpiObsModels", "PoissonError", "evaluation", "standard"] 1.218 μs (5%) 1.38 KiB (1%) 18
["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 3.586 μs (5%) 7.75 KiB (1%) 31
["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 2.913 μs (5%) 4.52 KiB (1%) 25
["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 136.213 μs (5%) 91.00 KiB (1%) 1913
["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 24.816 μs (5%) 29.25 KiB (1%) 712
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["EpiObsModels", "PrefixObservationModel", "evaluation", "standard"] 1.611 μs (5%) 1.44 KiB (1%) 26
["EpiObsModels", "PrefixObservationModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 1.867 μs (5%) 1.66 KiB (1%) 31
["EpiObsModels", "PrefixObservationModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.809 μs (5%) 1.66 KiB (1%) 31
["EpiObsModels", "PrefixObservationModel", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 21.941 μs (5%) 12.91 KiB (1%) 283
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["EpiObsModels", "StackObservationModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 7.865 μs (5%) 5.83 KiB (1%) 100
["EpiObsModels", "StackObservationModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 7.769 μs (5%) 5.83 KiB (1%) 100
["EpiObsModels", "StackObservationModels", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 58.819 μs (5%) 49.23 KiB (1%) 1020
["EpiObsModels", "StackObservationModels", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 40.966 μs (5%) 44.02 KiB (1%) 911
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["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 5.654 μs (5%) 15.88 KiB (1%) 83
["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 5.382 μs (5%) 14.62 KiB (1%) 75
["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 79.918 μs (5%) 60.41 KiB (1%) 1139
["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 62.306 μs (5%) 53.94 KiB (1%) 1022
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["EpiObsModels", "observation_error", "missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 2.117 μs (5%) 4.03 KiB (1%) 38
["EpiObsModels", "observation_error", "missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.605 μs (5%) 2.47 KiB (1%) 28
["EpiObsModels", "observation_error", "missing obs", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 28.894 μs (5%) 24.73 KiB (1%) 490
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["EpiObsModels", "observation_error", "no missing obs", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 10.118 μs (5%) 12.83 KiB (1%) 286
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["EpiObsModels", "observation_error", "partially missing obs", "evaluation", "standard"] 1.673 μs (5%) 1.73 KiB (1%) 25
["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 1.678 μs (5%) 2.22 KiB (1%) 26
["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.515 μs (5%) 1.91 KiB (1%) 24
["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 38.352 μs (5%) 23.89 KiB (1%) 499
["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 23.223 μs (5%) 17.69 KiB (1%) 369
["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 2.348 μs (5%) 112 bytes (1%) 2
["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 2.114 μs (5%) 112 bytes (1%) 2

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

  • ["EpiAwareUtils"]
  • ["EpiInfModels", "DirectInfections", "evaluation"]
  • ["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiInfModels", "ExpGrowthRate", "evaluation"]
  • ["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "AR", "evaluation"]
  • ["EpiLatentModels", "AR", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "AR", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "AR", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "BroadcastLatentModel", "evaluation"]
  • ["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "CombineLatentModels", "evaluation"]
  • ["EpiLatentModels", "CombineLatentModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "CombineLatentModels", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "CombineLatentModels", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "ConcatLatentModels", "evaluation"]
  • ["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "DiffLatentModel", "evaluation"]
  • ["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "HierarchicalNormal", "evaluation"]
  • ["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "Intercept", "evaluation"]
  • ["EpiLatentModels", "Intercept", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "Intercept", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "Intercept", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "PrefixLatentModel", "evaluation"]
  • ["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "RandomWalk", "evaluation"]
  • ["EpiLatentModels", "RandomWalk", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "RandomWalk", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "RandomWalk", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "RecordExpectedLatent", "evaluation"]
  • ["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "TransformLatentModel", "evaluation"]
  • ["EpiLatentModels", "TransformLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "TransformLatentModel", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "TransformLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "broadcast_dayofweek", "evaluation"]
  • ["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "broadcast_weekly", "evaluation"]
  • ["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "Ascertainment", "evaluation"]
  • ["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "LatentDelay", "evaluation"]
  • ["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "NegativeBinomialError", "evaluation"]
  • ["EpiObsModels", "NegativeBinomialError", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "NegativeBinomialError", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "NegativeBinomialError", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "PoissonError", "evaluation"]
  • ["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "PrefixObservationModel", "evaluation"]
  • ["EpiObsModels", "PrefixObservationModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "PrefixObservationModel", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "PrefixObservationModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "StackObservationModels", "evaluation"]
  • ["EpiObsModels", "StackObservationModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "StackObservationModels", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "StackObservationModels", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "ascertainment_dayofweek", "evaluation"]
  • ["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "observation_error", "missing obs", "evaluation"]
  • ["EpiObsModels", "observation_error", "missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "observation_error", "missing obs", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "observation_error", "missing obs", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "observation_error", "no missing obs", "evaluation"]
  • ["EpiObsModels", "observation_error", "no missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "observation_error", "no missing obs", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "observation_error", "no missing obs", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "observation_error", "partially missing obs", "evaluation"]
  • ["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]

Julia versioninfo

Julia Version 1.10.5
Commit 6f3fdf7b362 (2024-08-27 14:19 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.5 LTS
  uname: Linux 6.8.0-1014-azure #16~22.04.1-Ubuntu SMP Thu Aug 15 21:31:41 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3003 MHz       5338 s          0 s        571 s      12185 s          0 s
       #2  3240 MHz       5433 s          0 s        604 s      12052 s          0 s
       #3  3016 MHz       4444 s          0 s        504 s      13146 s          0 s
       #4  2606 MHz       5215 s          0 s        473 s      12409 s          0 s
  Memory: 15.615272521972656 GB (12372.41796875 MB free)
  Uptime: 1813.95 sec
  Load Avg:  1.0  1.0  1.0
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Baseline result

Benchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewal

Job Properties

  • Time of benchmark: 4 Oct 2024 - 11:48
  • Package commit: 21fb99
  • Julia commit: 6f3fdf
  • Julia command flags: None
  • Environment variables: None

Results

Below is a table of this job's results, obtained by running the benchmarks.
The values listed in the ID column have the structure [parent_group, child_group, ..., key], and can be used to
index into the BaseBenchmarks suite to retrieve the corresponding benchmarks.
The percentages accompanying time and memory values in the below table are noise tolerances. The "true"
time/memory value for a given benchmark is expected to fall within this percentage of the reported value.
An empty cell means that the value was zero.

ID time GC time memory allocations
["EpiAwareUtils", "censored_pmf"] 2.046 μs (5%) 416 bytes (1%) 5
["EpiInfModels", "DirectInfections", "evaluation", "linked"] 290.170 ns (5%) 432 bytes (1%) 7
["EpiInfModels", "DirectInfections", "evaluation", "standard"] 297.257 ns (5%) 432 bytes (1%) 7
["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 423.352 ns (5%) 784 bytes (1%) 13
["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 428.432 ns (5%) 784 bytes (1%) 13
["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 9.137 μs (5%) 5.62 KiB (1%) 115
["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 9.257 μs (5%) 5.62 KiB (1%) 115
["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 553.273 ns (5%) 272 bytes (1%) 6
["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 559.599 ns (5%) 272 bytes (1%) 6
["EpiInfModels", "ExpGrowthRate", "evaluation", "linked"] 210.521 ns (5%) 256 bytes (1%) 4
["EpiInfModels", "ExpGrowthRate", "evaluation", "standard"] 210.895 ns (5%) 256 bytes (1%) 4
["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 307.421 ns (5%) 512 bytes (1%) 9
["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 304.416 ns (5%) 512 bytes (1%) 9
["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 9.197 μs (5%) 5.64 KiB (1%) 114
["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 9.208 μs (5%) 5.64 KiB (1%) 114
["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 553.219 ns (5%) 272 bytes (1%) 6
["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 544.846 ns (5%) 272 bytes (1%) 6
["EpiLatentModels", "AR", "evaluation", "linked"] 2.020 μs (5%) 3.84 KiB (1%) 45
["EpiLatentModels", "AR", "evaluation", "standard"] 1.593 μs (5%) 2.80 KiB (1%) 38
["EpiLatentModels", "AR", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 3.345 μs (5%) 11.69 KiB (1%) 55
["EpiLatentModels", "AR", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 2.888 μs (5%) 10.12 KiB (1%) 46
["EpiLatentModels", "AR", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 104.795 μs (5%) 55.31 KiB (1%) 1113
["EpiLatentModels", "AR", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 68.217 μs (5%) 40.64 KiB (1%) 818
["EpiLatentModels", "AR", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 17.111 μs (5%) 8.44 KiB (1%) 225
["EpiLatentModels", "AR", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 15.639 μs (5%) 7.31 KiB (1%) 207
["EpiLatentModels", "BroadcastLatentModel", "evaluation", "linked"] 1.504 μs (5%) 3.05 KiB (1%) 34
["EpiLatentModels", "BroadcastLatentModel", "evaluation", "standard"] 1.250 μs (5%) 2.17 KiB (1%) 30
["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 1.939 μs (5%) 5.16 KiB (1%) 41
["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.660 μs (5%) 4.28 KiB (1%) 37
["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 43.020 μs (5%) 24.41 KiB (1%) 447
["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 27.711 μs (5%) 16.86 KiB (1%) 333
["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 3.002 μs (5%) 1.00 KiB (1%) 27
["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 2.731 μs (5%) 1.00 KiB (1%) 27
["EpiLatentModels", "CombineLatentModels", "evaluation", "linked"] 63.218 μs (5%) 52.27 KiB (1%) 580
["EpiLatentModels", "CombineLatentModels", "evaluation", "standard"] 57.917 μs (5%) 37.69 KiB (1%) 536
["EpiLatentModels", "CombineLatentModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 129.731 μs (5%) 119.19 KiB (1%) 1184
["EpiLatentModels", "CombineLatentModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 122.107 μs (5%) 89.31 KiB (1%) 1092
["EpiLatentModels", "CombineLatentModels", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 187.198 μs (5%) 107.81 KiB (1%) 1710
["EpiLatentModels", "CombineLatentModels", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 144.719 μs (5%) 79.61 KiB (1%) 1378
["EpiLatentModels", "CombineLatentModels", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 18.043 μs (5%) 8.58 KiB (1%) 226
["EpiLatentModels", "CombineLatentModels", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 16.350 μs (5%) 7.45 KiB (1%) 208
["EpiLatentModels", "ConcatLatentModels", "evaluation", "linked"] 11.151 μs (5%) 30.39 KiB (1%) 214
["EpiLatentModels", "ConcatLatentModels", "evaluation", "standard"] 8.927 μs (5%) 21.95 KiB (1%) 184
["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 12.914 μs (5%) 34.09 KiB (1%) 224
["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 10.229 μs (5%) 25.66 KiB (1%) 194
["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 72.524 μs (5%) 56.38 KiB (1%) 719
["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 51.315 μs (5%) 42.72 KiB (1%) 580
["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 5.181 μs (5%) 2.19 KiB (1%) 52
["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 5.179 μs (5%) 2.19 KiB (1%) 52
["EpiLatentModels", "DiffLatentModel", "evaluation", "linked"] 1.732 μs (5%) 4.17 KiB (1%) 37
["EpiLatentModels", "DiffLatentModel", "evaluation", "standard"] 1.331 μs (5%) 2.48 KiB (1%) 31
["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 2.878 μs (5%) 12.62 KiB (1%) 45
["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 2.420 μs (5%) 10.94 KiB (1%) 39
["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 57.166 μs (5%) 38.81 KiB (1%) 748
["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 41.718 μs (5%) 31.91 KiB (1%) 633
["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 6.985 μs (5%) 2.22 KiB (1%) 51
["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 6.450 μs (5%) 2.22 KiB (1%) 51
["EpiLatentModels", "HierarchicalNormal", "evaluation", "linked"] 414.588 ns (5%) 1.00 KiB (1%) 8
["EpiLatentModels", "HierarchicalNormal", "evaluation", "standard"] 358.238 ns (5%) 864 bytes (1%) 7
["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 940.800 ns (5%) 5.28 KiB (1%) 14
["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 879.600 ns (5%) 5.12 KiB (1%) 13
["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 41.377 μs (5%) 19.83 KiB (1%) 376
["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 26.279 μs (5%) 14.45 KiB (1%) 266
["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 1.234 μs (5%) 656 bytes (1%) 11
["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 1.055 μs (5%) 656 bytes (1%) 11
["EpiLatentModels", "Intercept", "evaluation", "linked"] 255.307 ns (5%) 336 bytes (1%) 5
["EpiLatentModels", "Intercept", "evaluation", "standard"] 258.520 ns (5%) 336 bytes (1%) 5
["EpiLatentModels", "Intercept", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 345.023 ns (5%) 640 bytes (1%) 10
["EpiLatentModels", "Intercept", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 344.645 ns (5%) 640 bytes (1%) 10
["EpiLatentModels", "Intercept", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 4.242 μs (5%) 3.53 KiB (1%) 76
["EpiLatentModels", "Intercept", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 4.298 μs (5%) 3.53 KiB (1%) 76
["EpiLatentModels", "Intercept", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 459.071 ns (5%) 240 bytes (1%) 3
["EpiLatentModels", "Intercept", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 465.990 ns (5%) 240 bytes (1%) 3
["EpiLatentModels", "PrefixLatentModel", "evaluation", "linked"] 1.899 μs (5%) 3.47 KiB (1%) 30
["EpiLatentModels", "PrefixLatentModel", "evaluation", "standard"] 1.713 μs (5%) 3.00 KiB (1%) 27
["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 2.486 μs (5%) 7.75 KiB (1%) 36
["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 2.164 μs (5%) 7.28 KiB (1%) 33
["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 44.362 μs (5%) 22.16 KiB (1%) 397
["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 28.843 μs (5%) 16.47 KiB (1%) 285
["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 1.237 μs (5%) 656 bytes (1%) 11
["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 1.061 μs (5%) 656 bytes (1%) 11
["EpiLatentModels", "RandomWalk", "evaluation", "linked"] 865.213 ns (5%) 1.86 KiB (1%) 18
["EpiLatentModels", "RandomWalk", "evaluation", "standard"] 769.585 ns (5%) 1.42 KiB (1%) 16
["EpiLatentModels", "RandomWalk", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 1.711 μs (5%) 8.73 KiB (1%) 25
["EpiLatentModels", "RandomWalk", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.669 μs (5%) 8.30 KiB (1%) 23
["EpiLatentModels", "RandomWalk", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 43.692 μs (5%) 26.19 KiB (1%) 487
["EpiLatentModels", "RandomWalk", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 29.225 μs (5%) 20.53 KiB (1%) 376
["EpiLatentModels", "RandomWalk", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 3.659 μs (5%) 1.31 KiB (1%) 27
["EpiLatentModels", "RandomWalk", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 3.346 μs (5%) 1.31 KiB (1%) 27
["EpiLatentModels", "RecordExpectedLatent", "evaluation", "linked"] 574.637 ns (5%) 1.19 KiB (1%) 12
["EpiLatentModels", "RecordExpectedLatent", "evaluation", "standard"] 471.740 ns (5%) 896 bytes (1%) 10
["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 809.195 ns (5%) 1.72 KiB (1%) 18
["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 671.870 ns (5%) 1.41 KiB (1%) 16
["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 40.866 μs (5%) 19.08 KiB (1%) 380
["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 26.540 μs (5%) 13.55 KiB (1%) 269
["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 1.144 μs (5%) 400 bytes (1%) 11
["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 974.667 ns (5%) 400 bytes (1%) 11
["EpiLatentModels", "TransformLatentModel", "evaluation", "linked"] 307.183 ns (5%) 384 bytes (1%) 6
["EpiLatentModels", "TransformLatentModel", "evaluation", "standard"] 306.528 ns (5%) 384 bytes (1%) 6
["EpiLatentModels", "TransformLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 403.700 ns (5%) 704 bytes (1%) 11
["EpiLatentModels", "TransformLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 404.000 ns (5%) 704 bytes (1%) 11
["EpiLatentModels", "TransformLatentModel", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 4.467 μs (5%) 3.84 KiB (1%) 81
["EpiLatentModels", "TransformLatentModel", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 4.521 μs (5%) 3.84 KiB (1%) 81
["EpiLatentModels", "TransformLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 522.382 ns (5%) 192 bytes (1%) 3
["EpiLatentModels", "TransformLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 529.453 ns (5%) 192 bytes (1%) 3
["EpiLatentModels", "broadcast_dayofweek", "evaluation", "linked"] 1.952 μs (5%) 4.16 KiB (1%) 44
["EpiLatentModels", "broadcast_dayofweek", "evaluation", "standard"] 1.605 μs (5%) 2.84 KiB (1%) 38
["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 2.711 μs (5%) 10.00 KiB (1%) 51
["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 2.378 μs (5%) 8.69 KiB (1%) 45
["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 56.886 μs (5%) 35.58 KiB (1%) 689
["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 39.844 μs (5%) 29.05 KiB (1%) 574
["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 5.071 μs (5%) 1.22 KiB (1%) 27
["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 4.906 μs (5%) 1.22 KiB (1%) 27
["EpiLatentModels", "broadcast_weekly", "evaluation", "linked"] 2.167 μs (5%) 4.52 KiB (1%) 47
["EpiLatentModels", "broadcast_weekly", "evaluation", "standard"] 1.610 μs (5%) 2.62 KiB (1%) 37
["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 2.812 μs (5%) 7.69 KiB (1%) 57
["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 2.230 μs (5%) 5.53 KiB (1%) 45
["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 82.052 μs (5%) 41.95 KiB (1%) 771
["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 46.526 μs (5%) 28.44 KiB (1%) 513
["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 5.278 μs (5%) 1.81 KiB (1%) 49
["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 4.643 μs (5%) 1.69 KiB (1%) 47
["EpiObsModels", "Ascertainment", "evaluation", "linked"] 3.370 μs (5%) 3.42 KiB (1%) 49
["EpiObsModels", "Ascertainment", "evaluation", "standard"] 3.319 μs (5%) 3.42 KiB (1%) 49
["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 4.110 μs (5%) 3.77 KiB (1%) 56
["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 4.103 μs (5%) 3.77 KiB (1%) 56
["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 48.130 μs (5%) 39.05 KiB (1%) 905
["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 34.083 μs (5%) 33.83 KiB (1%) 796
["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 5.734 μs (5%) 96 bytes (1%) 2
["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 5.657 μs (5%) 96 bytes (1%) 2
["EpiObsModels", "LatentDelay", "evaluation", "linked"] 16.260 μs (5%) 22.14 KiB (1%) 206
["EpiObsModels", "LatentDelay", "evaluation", "standard"] 16.230 μs (5%) 22.14 KiB (1%) 206
["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 21.971 μs (5%) 22.36 KiB (1%) 211
["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 21.110 μs (5%) 22.36 KiB (1%) 211
["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 290.350 μs (5%) 293.61 KiB (1%) 6804
["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 272.136 μs (5%) 288.39 KiB (1%) 6695
["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 54.170 μs (5%) 96 bytes (1%) 2
["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 55.342 μs (5%) 96 bytes (1%) 2
["EpiObsModels", "NegativeBinomialError", "evaluation", "linked"] 1.149 μs (5%) 336 bytes (1%) 5
["EpiObsModels", "NegativeBinomialError", "evaluation", "standard"] 1.121 μs (5%) 336 bytes (1%) 5
["EpiObsModels", "NegativeBinomialError", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 1.840 μs (5%) 560 bytes (1%) 10
["EpiObsModels", "NegativeBinomialError", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.707 μs (5%) 560 bytes (1%) 10
["EpiObsModels", "NegativeBinomialError", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 44.602 μs (5%) 36.33 KiB (1%) 899
["EpiObsModels", "NegativeBinomialError", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 30.286 μs (5%) 31.11 KiB (1%) 790
["EpiObsModels", "NegativeBinomialError", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 5.834 μs (5%) 96 bytes (1%) 2
["EpiObsModels", "NegativeBinomialError", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 5.681 μs (5%) 96 bytes (1%) 2
["EpiObsModels", "PoissonError", "evaluation", "linked"] 1.554 μs (5%) 1.80 KiB (1%) 22
["EpiObsModels", "PoissonError", "evaluation", "standard"] 1.203 μs (5%) 1.38 KiB (1%) 18
["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 3.190 μs (5%) 7.75 KiB (1%) 31
["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 2.559 μs (5%) 4.52 KiB (1%) 25
["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 133.348 μs (5%) 91.00 KiB (1%) 1913
["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 23.704 μs (5%) 29.25 KiB (1%) 712
["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 6.282 μs (5%) 176 bytes (1%) 2
["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 4.458 μs (5%) 176 bytes (1%) 2
["EpiObsModels", "PrefixObservationModel", "evaluation", "linked"] 1.661 μs (5%) 1.44 KiB (1%) 26
["EpiObsModels", "PrefixObservationModel", "evaluation", "standard"] 1.635 μs (5%) 1.44 KiB (1%) 26
["EpiObsModels", "PrefixObservationModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 1.829 μs (5%) 1.66 KiB (1%) 31
["EpiObsModels", "PrefixObservationModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.773 μs (5%) 1.66 KiB (1%) 31
["EpiObsModels", "PrefixObservationModel", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 22.031 μs (5%) 12.91 KiB (1%) 283
["EpiObsModels", "PrefixObservationModel", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 8.332 μs (5%) 7.69 KiB (1%) 174
["EpiObsModels", "PrefixObservationModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 1.234 μs (5%) 96 bytes (1%) 2
["EpiObsModels", "PrefixObservationModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 1.081 μs (5%) 96 bytes (1%) 2
["EpiObsModels", "StackObservationModels", "evaluation", "linked"] 7.018 μs (5%) 5.48 KiB (1%) 93
["EpiObsModels", "StackObservationModels", "evaluation", "standard"] 6.948 μs (5%) 5.48 KiB (1%) 93
["EpiObsModels", "StackObservationModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 7.859 μs (5%) 5.83 KiB (1%) 100
["EpiObsModels", "StackObservationModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 7.819 μs (5%) 5.83 KiB (1%) 100
["EpiObsModels", "StackObservationModels", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 58.628 μs (5%) 49.23 KiB (1%) 1020
["EpiObsModels", "StackObservationModels", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 40.845 μs (5%) 44.02 KiB (1%) 911
["EpiObsModels", "StackObservationModels", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 6.254 μs (5%) 96 bytes (1%) 2
["EpiObsModels", "StackObservationModels", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 6.091 μs (5%) 96 bytes (1%) 2
["EpiObsModels", "ascertainment_dayofweek", "evaluation", "linked"] 4.341 μs (5%) 8.88 KiB (1%) 75
["EpiObsModels", "ascertainment_dayofweek", "evaluation", "standard"] 4.123 μs (5%) 7.62 KiB (1%) 67
["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 5.467 μs (5%) 15.88 KiB (1%) 83
["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 5.046 μs (5%) 14.62 KiB (1%) 75
["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 79.127 μs (5%) 60.41 KiB (1%) 1139
["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 61.394 μs (5%) 53.94 KiB (1%) 1022
["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 5.607 μs (5%) 544 bytes (1%) 11
["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 5.797 μs (5%) 544 bytes (1%) 11
["EpiObsModels", "observation_error", "missing obs", "evaluation", "linked"] 1.541 μs (5%) 2.97 KiB (1%) 31
["EpiObsModels", "observation_error", "missing obs", "evaluation", "standard"] 1.014 μs (5%) 1.41 KiB (1%) 21
["EpiObsModels", "observation_error", "missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 2.129 μs (5%) 4.03 KiB (1%) 38
["EpiObsModels", "observation_error", "missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.583 μs (5%) 2.47 KiB (1%) 28
["EpiObsModels", "observation_error", "missing obs", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 27.871 μs (5%) 24.73 KiB (1%) 490
["EpiObsModels", "observation_error", "missing obs", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 13.535 μs (5%) 17.28 KiB (1%) 352
["EpiObsModels", "observation_error", "missing obs", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 2.291 μs (5%) 144 bytes (1%) 2
["EpiObsModels", "observation_error", "missing obs", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 2.024 μs (5%) 144 bytes (1%) 2
["EpiObsModels", "observation_error", "no missing obs", "evaluation", "linked"] 444.212 ns (5%) 288 bytes (1%) 5
["EpiObsModels", "observation_error", "no missing obs", "evaluation", "standard"] 411.819 ns (5%) 288 bytes (1%) 5
["EpiObsModels", "observation_error", "no missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 572.641 ns (5%) 512 bytes (1%) 10
["EpiObsModels", "observation_error", "no missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 523.521 ns (5%) 512 bytes (1%) 10
["EpiObsModels", "observation_error", "no missing obs", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 23.103 μs (5%) 18.72 KiB (1%) 414
["EpiObsModels", "observation_error", "no missing obs", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 10.290 μs (5%) 12.83 KiB (1%) 286
["EpiObsModels", "observation_error", "no missing obs", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 2.050 μs (5%) 96 bytes (1%) 2
["EpiObsModels", "observation_error", "no missing obs", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 1.675 μs (5%) 96 bytes (1%) 2
["EpiObsModels", "observation_error", "partially missing obs", "evaluation", "linked"] 1.800 μs (5%) 2.05 KiB (1%) 27
["EpiObsModels", "observation_error", "partially missing obs", "evaluation", "standard"] 1.659 μs (5%) 1.73 KiB (1%) 25
["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "linked"] 1.712 μs (5%) 2.22 KiB (1%) 26
["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)", "standard"] 1.537 μs (5%) 1.91 KiB (1%) 24
["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoReverseDiff()", "linked"] 37.840 μs (5%) 23.89 KiB (1%) 499
["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoReverseDiff()", "standard"] 22.812 μs (5%) 17.69 KiB (1%) 369
["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "linked"] 2.274 μs (5%) 112 bytes (1%) 2
["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoReverseDiff(compile=true)", "standard"] 2.077 μs (5%) 112 bytes (1%) 2

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

  • ["EpiAwareUtils"]
  • ["EpiInfModels", "DirectInfections", "evaluation"]
  • ["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiInfModels", "DirectInfections", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiInfModels", "ExpGrowthRate", "evaluation"]
  • ["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiInfModels", "ExpGrowthRate", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "AR", "evaluation"]
  • ["EpiLatentModels", "AR", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "AR", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "AR", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "BroadcastLatentModel", "evaluation"]
  • ["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "BroadcastLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "CombineLatentModels", "evaluation"]
  • ["EpiLatentModels", "CombineLatentModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "CombineLatentModels", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "CombineLatentModels", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "ConcatLatentModels", "evaluation"]
  • ["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "ConcatLatentModels", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "DiffLatentModel", "evaluation"]
  • ["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "DiffLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "HierarchicalNormal", "evaluation"]
  • ["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "HierarchicalNormal", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "Intercept", "evaluation"]
  • ["EpiLatentModels", "Intercept", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "Intercept", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "Intercept", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "PrefixLatentModel", "evaluation"]
  • ["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "PrefixLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "RandomWalk", "evaluation"]
  • ["EpiLatentModels", "RandomWalk", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "RandomWalk", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "RandomWalk", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "RecordExpectedLatent", "evaluation"]
  • ["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "RecordExpectedLatent", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "TransformLatentModel", "evaluation"]
  • ["EpiLatentModels", "TransformLatentModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "TransformLatentModel", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "TransformLatentModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "broadcast_dayofweek", "evaluation"]
  • ["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "broadcast_dayofweek", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiLatentModels", "broadcast_weekly", "evaluation"]
  • ["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiLatentModels", "broadcast_weekly", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "Ascertainment", "evaluation"]
  • ["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "Ascertainment", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "LatentDelay", "evaluation"]
  • ["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "LatentDelay", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "NegativeBinomialError", "evaluation"]
  • ["EpiObsModels", "NegativeBinomialError", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "NegativeBinomialError", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "NegativeBinomialError", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "PoissonError", "evaluation"]
  • ["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "PoissonError", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "PrefixObservationModel", "evaluation"]
  • ["EpiObsModels", "PrefixObservationModel", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "PrefixObservationModel", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "PrefixObservationModel", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "StackObservationModels", "evaluation"]
  • ["EpiObsModels", "StackObservationModels", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "StackObservationModels", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "StackObservationModels", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "ascertainment_dayofweek", "evaluation"]
  • ["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "ascertainment_dayofweek", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "observation_error", "missing obs", "evaluation"]
  • ["EpiObsModels", "observation_error", "missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "observation_error", "missing obs", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "observation_error", "missing obs", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "observation_error", "no missing obs", "evaluation"]
  • ["EpiObsModels", "observation_error", "no missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "observation_error", "no missing obs", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "observation_error", "no missing obs", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]
  • ["EpiObsModels", "observation_error", "partially missing obs", "evaluation"]
  • ["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoForwardDiff(chunksize=0)"]
  • ["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoReverseDiff()"]
  • ["EpiObsModels", "observation_error", "partially missing obs", "gradient", "ADTypes.AutoReverseDiff(compile=true)"]

Julia versioninfo

Julia Version 1.10.5
Commit 6f3fdf7b362 (2024-08-27 14:19 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.5 LTS
  uname: Linux 6.8.0-1014-azure #16~22.04.1-Ubuntu SMP Thu Aug 15 21:31:41 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2445 MHz       7958 s          0 s        910 s      23623 s          0 s
       #2  3243 MHz       8018 s          0 s        955 s      23514 s          0 s
       #3  3236 MHz       7442 s          0 s        868 s      24186 s          0 s
       #4  3184 MHz      10452 s          0 s        906 s      21144 s          0 s
  Memory: 15.615272521972656 GB (12376.49609375 MB free)
  Uptime: 3255.83 sec
  Load Avg:  1.02  1.04  1.0
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Runtime information

Runtime Info
BLAS #threads 2
BLAS.vendor() lbt
Sys.CPU_THREADS 4

lscpu output:

Architecture:                         x86_64
CPU op-mode(s):                       32-bit, 64-bit
Address sizes:                        48 bits physical, 48 bits virtual
Byte Order:                           Little Endian
CPU(s):                               4
On-line CPU(s) list:                  0-3
Vendor ID:                            AuthenticAMD
Model name:                           AMD EPYC 7763 64-Core Processor
CPU family:                           25
Model:                                1
Thread(s) per core:                   2
Core(s) per socket:                   2
Socket(s):                            1
Stepping:                             1
BogoMIPS:                             4890.85
Flags:                                fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl tsc_reliable nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm cmp_legacy svm cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw topoext vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves user_shstk clzero xsaveerptr rdpru arat npt nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold v_vmsave_vmload umip vaes vpclmulqdq rdpid fsrm
Virtualization:                       AMD-V
Hypervisor vendor:                    Microsoft
Virtualization type:                  full
L1d cache:                            64 KiB (2 instances)
L1i cache:                            64 KiB (2 instances)
L2 cache:                             1 MiB (2 instances)
L3 cache:                             32 MiB (1 instance)
NUMA node(s):                         1
NUMA node0 CPU(s):                    0-3
Vulnerability Gather data sampling:   Not affected
Vulnerability Itlb multihit:          Not affected
Vulnerability L1tf:                   Not affected
Vulnerability Mds:                    Not affected
Vulnerability Meltdown:               Not affected
Vulnerability Mmio stale data:        Not affected
Vulnerability Reg file data sampling: Not affected
Vulnerability Retbleed:               Not affected
Vulnerability Spec rstack overflow:   Vulnerable: Safe RET, no microcode
Vulnerability Spec store bypass:      Vulnerable
Vulnerability Spectre v1:             Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2:             Mitigation; Retpolines; STIBP disabled; RSB filling; PBRSB-eIBRS Not affected; BHI Not affected
Vulnerability Srbds:                  Not affected
Vulnerability Tsx async abort:        Not affected
Cpu Property Value
Brand AMD EPYC 7763 64-Core Processor
Vendor :AMD
Architecture :Unknown
Model Family: 0xaf, Model: 0x01, Stepping: 0x01, Type: 0x00
Cores 16 physical cores, 16 logical cores (on executing CPU)
No Hyperthreading hardware capability detected
Clock Frequencies Not supported by CPU
Data Cache Level 1:3 : (32, 512, 32768) kbytes
64 byte cache line size
Address Size 48 bits virtual, 48 bits physical
SIMD 256 bit = 32 byte max. SIMD vector size
Time Stamp Counter TSC is accessible via rdtsc
TSC runs at constant rate (invariant from clock frequency)
Perf. Monitoring Performance Monitoring Counters (PMC) are not supported
Hypervisor Yes, Microsoft

@seabbs
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seabbs commented Oct 4, 2024

So this has a different pattern of impact vs #470.

Here I see slower evaluation and forward diff, no real impact on reversediff with compilation and much faster reverse diff.

Is this due to a specialisation that exists for accumulate do we think or other?

I think this one is worth changing given these results (this makes me want to get Enzyme and Tapir into the benchmarks asap)

@SamuelBrand1
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Is this due to a specialisation that exists for accumulate do we think or other?

This is possible, but cumsum calls down to accumulate! which I'd imagine has similar things happening.

My mental model was that accumulate saves either a broadcast sum or a vcat by using the init keyword arg... but I'm not sure thats the win I thought it would be now.

@SamuelBrand1 SamuelBrand1 mentioned this pull request Oct 4, 2024
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3 participants
@seabbs @codecov-commenter @SamuelBrand1