perf: speedup fasta reader #296
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Here I restructured `FastaReader::read()` function to avoid extra allocations. This is basically a complete rewrite. This involved changing error handling, so I thought while we are at it, why not improve error messages. While working on the new algo, I also discovered a few important cases missing from tests, so I added them. Speedup on mpox-500 run: ~29% Command: ``` $ cargo -q build --release --target-dir=/workdir/.build/docker --bin=treetime $ hyperfine --warmup 1 --show-output '/workdir/.build/docker/release/treetime ancestral --method-anc=parsimony --dense=false --tree=data/mpox/clade-ii/500/tree.nwk --outdir=tmp/smoke-tests/ancestral/marginal/mpox/clade-ii/500 data/mpox/clade-ii/500/aln.fasta.xz' ``` Before (branch: rust, commit f676392): ``` Time (mean ± σ): 1.866 s ± 0.113 s [User: 4.547 s, System: 0.576 s] Range (min … max): 1.768 s … 2.041 s 10 runs ``` After: ``` Time (mean ± σ): 1.444 s ± 0.111 s [User: 4.181 s, System: 0.527 s] Range (min … max): 1.341 s … 1.650 s 10 runs ``` Profiler shows that `treetime::io::fasta::FastaReader::read()` now takes ~18% of the program, down from 25% (in single-threaded mode).
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Here I restructured
FastaReader::read()function to avoid extra allocations. This is basically a complete rewrite.This involved changing error handling, so I thought while we are at it, why not improve error messages.
While working on the new algo, I also discovered a few important cases missing from tests, so I added them.
Speedup on mpox-500 run: ~29%
Command:
Before (branch: rust, commit f676392):
After:
Profiler shows that
treetime::io::fasta::FastaReader::read()now takes ~18% of the program, down from 25% (in single-threaded mode).