Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Perf/loop over kids first #297

Merged
merged 3 commits into from
Dec 10, 2024
Merged

Perf/loop over kids first #297

merged 3 commits into from
Dec 10, 2024

Conversation

rneher
Copy link
Member

@rneher rneher commented Dec 10, 2024

small experiment: this is a bit faster for me

richard@X1-2024:~/Projects_GitHub/TreeTime/treetime_rs$ hyperfine --warmup 1 --show-output 'target/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'                
Benchmark 1: target/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                                                                                                                                                                                                          
  Time (mean ± σ):      1.016 s ±  0.025 s    [User: 2.100 s, System: 2.086 s]                                                                                                                                     
  Range (min … max):    0.980 s …  1.064 s    10 runs                                                                                                                                                              

vs

richard@X1-2024:~/Projects_GitHub/TreeTime/treetime_rs$ hyperfine --warmup 1 --show-output 'target/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'                
Benchmark 1: target/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                                                                                                
  Time (mean ± σ):      1.157 s ±  0.027 s    [User: 3.124 s, System: 2.120 s]                           
  Range (min … max):    1.124 s …  1.198 s    10 runs                                                    

not really worth the trouble unless you feel it is cleaner...

@ivan-aksamentov ivan-aksamentov merged commit 01f78d6 into rust Dec 10, 2024
14 checks passed
@ivan-aksamentov ivan-aksamentov deleted the perf/loop-over-kids-first branch December 10, 2024 21:22
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants