[BioRuby] Benchmarking FASTA file parsing
Tomoaki NISHIYAMA
tomoakin at kenroku.kanazawa-u.ac.jp
Fri Aug 13 13:37:06 UTC 2010
Hi,
The benchmark is interesting.
> Is it possible to optimize the code without major rewriting?
Using ruby 1.9.2 (RC2) makes it 2.6 times faster without any rewriting
the bioruby parser code :)
compared to ruby-1.8 (1.8.7-p299).
$ ~/ruby192/bin/ruby benchfasta
user system total real
Hack 3.800000 0.000000 3.800000 ( 3.800830)
Bio 13.090000 0.000000 13.090000 ( 13.095722)
$ ~/ruby187/bin/ruby benchfasta
user system total real
Hack 7.460000 0.000000 7.460000 ( 7.456281)
Bio 34.670000 0.000000 34.670000 ( 34.680271)
As you stated 3 times faster with the hack, you may be already using
ruby 1.9.
Anyway, I think 13 or 18 seconds for 100 M entry is fast enough and this
part will not be the bottle neck of any application.
How fast do you need it be?
--
Tomoaki NISHIYAMA
Advanced Science Research Center,
Kanazawa University,
13-1 Takara-machi,
Kanazawa, 920-0934, Japan
More information about the BioRuby
mailing list