4 ms·

Take away those last three benchmarks (spectral-norm, fasta & binary-trees) then things do look quite different. For eg: Here is Which programs are best with t

Take away those last three benchmarks (spectral-norm, fasta & binary-trees) then things do look quite different. For eg: Here is Which programs are best with those benchmarks removed: http://benchmarksgame.alioth.debian.org/u32/which-programs-are-best.php?gpp=on&ifc=on&java=on&ghc=on&sbcl=on&csharp=on&v8=on&dart=on&hipe=on&lua=on&vw=on&php=on&jruby=on&python3=on&perl=on&xfullcpu=1&xmem=0&xloc=0&nbody=1&fannkuchredux=1&meteor=0&fasta=0&fastaredux=1&spectralnorm=0&revcomp=1&mandelbrot=1&knucleotide=1&regexdna=1&pidigits=1&chameneosredux=0&threadring=0&binarytreesredux=0&binarytrees=0&calc=chart http://benchmarksgame.alioth.debian.org/u32/which-programs-a... This shows Perl higher up the chart with it being 49% better (on average) than Ruby. Some other things to note: 1. Perl has never been fast with binary trees. But Ruby 1.8 is even worse (I recall it being many times slower than Perl at this). So hats off to the Ruby 1.9 VM guys because they've turned things around and now it's even out pacing Lua on this benchmark! - http://benchmarksgame.alioth.debian.org/u32/performance.php?test=binarytrees http://benchmarksgame.alioth.debian.org/u32/performance.php?... 2. Fasta in Ruby maybe twice quicker than Perl however it uses over 100 times more memory! This is be because it's inlining some code (eval) giving it a huge speed bump at expense of a bigger program footprint. If I do a port of this to Perl then this fasta.pl runs 2.6 times faster than alioth's perl version (which now means the Ruby version is about 30% slower than it's direct equivalent Perl version). 3. My make_repeat_fasta idiomatic subroutine is actually a little slower than the one in fasta.pl on alioth. So both my fasta.pl & alioth's fasta.rb programs could be speeded up more :) 4. I may even be able to shave a little bit more off fasta.pl time. Same might be true for spectral norm & binary-tree however the Perl versions aren't showing up on alioth site at moment :( ... IIRC, when I last looked at the perl binary-trees code on alioth a couple of years ago I was able to shave 10% off. ref: My perl port of fasta.rb on alioth - https://gist.github.com/4675254 https://gist.github.com/4675254

Mithaldu 14y ago
Frankly, i'm not convinced there's any point in investing time on improving the benchmarks there, considering the overall comparison directly contradicts the detailed comparison, by putting perl in a worse position than languages it outperforms.
- igouy 14y ago
  You don't seem to understand what the overall comparison shows. Are you familiar with descriptive statistics? Quartiles? Box plots?
  - Mithaldu 14y ago
    > You don't seem to understand what the overall comparison shows. I told you i don't. It looks entirely nonsensical. I asked you for clarification. So far your only response has been to parrot my saying that i don't understand why your data representations are dissonant. > Are you familiar with descriptive statistics? Possibly under another name, but i don't know what you mean when you say that. > Quartiles? In theory yes, i am unsure how you're applying it here, since we're not talking about binnable quantities. > Box plots? Yes.
    - igouy 14y ago
      >> I told you i don't. It looks entirely nonsensical. I asked you for clarification. So far your only response has been to parrot my saying that i don't understand why your data representations are dissonant. << It would have been better if you had said -- "English is not my primary languages and especially english maths are hard for me to grasp." -- instead of saying "it certainly seems deceptive". You say you are familiar with box plots, so you should have no difficulty understanding that box plot shows - the Perl and Ruby programs have very similar performance when compared to the fastest programs. "Visual Presentation of Data by Means of Box Plots" http://www.lcgceurope.com/lcgceurope/data/articlestandard/lcgceurope/132005/152912/article.pdf http://www.lcgceurope.com/lcgceurope/data/articlestandard/lc...
      - Mithaldu 14y ago
        Those two sentences are not a contradiction. I may not be good with reading english descriptions of math, but i am good with applied math. The calculations i did with your numbers disagree with what your graph showed. So to me the graph seems deceptive. There is no contradiction in this. Further, if you show me the actual calculations done, i will understand it perfectly fine. Yet you refuse to do so. I do not understand why, and i hope you can understand how that makes me even more distrustful. On the graph in the overview page Perl was shown to significantly outperform Ruby in a number of benchmarks, yes, i could see that. Yet the median of Perl was still set higher than the median of Ruby, which could possibly be explained by perl also being outperformed significantly in one benchmark, but which was not supported by the actual direct comparison numbers. So i ask again: Please show me the actual calculations performed to arrive at the median values shown in the overview graph.
igouy 14y ago
>> Take away those last three benchmarks... << What if we are selective with the evidence a different way, what if we take away k-nucleotide and pi-digits and reverse-complement :-) >> My perl port of fasta.rb << http://benchmarksgame.alioth.debian.org/play.php#contribute http://benchmarksgame.alioth.debian.org/play.php#contribute
- draegtun 14y ago
  On the contrary my dear igouy, specialisation can be key and knowing which tool in my toolset is best for different tasks is indeed insightful & helpful ;-) re: contribute - Looking on my hard disk I see that I downloaded the bencher/shootout-scm back on 1st Jan 2010. However IIRC the process of contributing code back was a bit unwieldy. If some free tuits come my way then I may relook at it.
  - igouy 14y ago
    Contributing code is a simple matter of attaching a complete tested source code file to a tracker item ticket. Really not difficult.
    - draegtun 14y ago
      Looking at my keychain I see I have three logins for alioth... draegtun, draegtun-guest & draegtun_guest... all created on 1st Jan 2010. So it looks like I had issues logging (back) onto Alioth at that time :( Anyway resolved it now because I see that draegtun-guest does work for me :) It's a little convoluted and the contribute notes don't initially match what you see at login but after rummaging around I found the required tracker and have now submitted the faster fasta.pl.

Mithaldu 14y ago

Frankly, i'm not convinced there's any point in investing time on improving the benchmarks there, considering the overall comparison directly contradicts the detailed comparison, by putting perl in a worse position than languages it outperforms.

igouy 14y ago
You don't seem to understand what the overall comparison shows. Are you familiar with descriptive statistics? Quartiles? Box plots?
- Mithaldu 14y ago
  > You don't seem to understand what the overall comparison shows. I told you i don't. It looks entirely nonsensical. I asked you for clarification. So far your only response has been to parrot my saying that i don't understand why your data representations are dissonant. > Are you familiar with descriptive statistics? Possibly under another name, but i don't know what you mean when you say that. > Quartiles? In theory yes, i am unsure how you're applying it here, since we're not talking about binnable quantities. > Box plots? Yes.
  - igouy 14y ago
    >> I told you i don't. It looks entirely nonsensical. I asked you for clarification. So far your only response has been to parrot my saying that i don't understand why your data representations are dissonant. << It would have been better if you had said -- "English is not my primary languages and especially english maths are hard for me to grasp." -- instead of saying "it certainly seems deceptive". You say you are familiar with box plots, so you should have no difficulty understanding that box plot shows - the Perl and Ruby programs have very similar performance when compared to the fastest programs. "Visual Presentation of Data by Means of Box Plots" http://www.lcgceurope.com/lcgceurope/data/articlestandard/lcgceurope/132005/152912/article.pdf http://www.lcgceurope.com/lcgceurope/data/articlestandard/lc...
    - Mithaldu 14y ago
      Those two sentences are not a contradiction. I may not be good with reading english descriptions of math, but i am good with applied math. The calculations i did with your numbers disagree with what your graph showed. So to me the graph seems deceptive. There is no contradiction in this. Further, if you show me the actual calculations done, i will understand it perfectly fine. Yet you refuse to do so. I do not understand why, and i hope you can understand how that makes me even more distrustful. On the graph in the overview page Perl was shown to significantly outperform Ruby in a number of benchmarks, yes, i could see that. Yet the median of Perl was still set higher than the median of Ruby, which could possibly be explained by perl also being outperformed significantly in one benchmark, but which was not supported by the actual direct comparison numbers. So i ask again: Please show me the actual calculations performed to arrive at the median values shown in the overview graph.

igouy 14y ago

>> Take away those last three benchmarks... << What if we are selective with the evidence a different way, what if we take away k-nucleotide and pi-digits and reverse-complement :-) >> My perl port of fasta.rb << http://benchmarksgame.alioth.debian.org/play.php#contribute http://benchmarksgame.alioth.debian.org/play.php#contribute

draegtun 14y ago
On the contrary my dear igouy, specialisation can be key and knowing which tool in my toolset is best for different tasks is indeed insightful & helpful ;-) re: contribute - Looking on my hard disk I see that I downloaded the bencher/shootout-scm back on 1st Jan 2010. However IIRC the process of contributing code back was a bit unwieldy. If some free tuits come my way then I may relook at it.
- igouy 14y ago
  Contributing code is a simple matter of attaching a complete tested source code file to a tracker item ticket. Really not difficult.
  - draegtun 14y ago
    Looking at my keychain I see I have three logins for alioth... draegtun, draegtun-guest & draegtun_guest... all created on 1st Jan 2010. So it looks like I had issues logging (back) onto Alioth at that time :( Anyway resolved it now because I see that draegtun-guest does work for me :) It's a little convoluted and the contribute notes don't initially match what you see at login but after rummaging around I found the required tracker and have now submitted the faster fasta.pl.