Repository navigation

Large scale perf - #194

Merged

jeromekelleher merged 19 commits into

tskit-dev:mainfrom

jeromekelleher:large-scale-perf

Sep 22, 2026

Merged

Large scale perf#194
jeromekelleher merged 19 commits into
tskit-dev:mainfrom
jeromekelleher:large-scale-perf

Commits on Sep 2, 2026
- Add a benchmark for genetic_value over the number of causal sites
  Jerome Kelleher
  committed
  43a3a38
- Accumulate genetic values in a single descent of the ARG
  Jerome Kelleher
  committed
  1cde68d
- Push causal mutation effects down the ARG in time order
  Jerome Kelleher
  committed
  ba5b2a6
- Hold the pending seeds of a node in a numba typed list
  Jerome Kelleher
  committed
  43f01c6
Commits on Sep 3, 2026
- Benchmark genetic_value on a simulation small enough to iterate on
  Jerome Kelleher
  committed
  f004ae3
- Make the individual level an output mapping of the descent
  Jerome Kelleher
  committed
  0273e8c
- Build the trees in numba, wired to nothing yet
  Jerome Kelleher
  committed
  ecef33f
- Send common causal alleles down a descent of the trees
  Jerome Kelleher
  committed
  b54570a
- Default to the descent, which measured faster everywhere
  Jerome Kelleher
  committed
  ec3e541
- Record what the descent does to the working set
  Jerome Kelleher
  committed
  8ffd22f
- Delete the push down, which lost to the descent everywhere
  Jerome Kelleher
  committed
  9b12346
- Interpret the tree building kernels under the nojit tests
  Jerome Kelleher
  committed
  9f0bb96
- Divide the causal sites between threads on request
  Jerome Kelleher
  committed
  aca6627
Commits on Sep 22, 2026
- Hand num_threads through sim_phenotype
  Jerome Kelleher
  committed
  97f0e48
- Stop checking in a benchmark baseline
  Jerome Kelleher
  committed
  13c0f9f
- Correct what the genetic value speedup is attributed to
  Jerome Kelleher
  committed
  a0d90d7
- Say why uniformly drawn causal sites cost so much more
  Jerome Kelleher
  committed
  bb2dbeb
- Cut the results out of the benchmark README
  Jerome Kelleher
  committed
  41bfb47
- Cut the changelog entries down to the house style
  Jerome Kelleher
  committed
  5b13346

Commits

Commits on Sep 2, 2026

Commits on Sep 3, 2026

Commits on Sep 22, 2026