Re: [TCLCORE] speed of tcl regexp

[Frédéric B. <fre...@fr...>]

Seems OK to me -- The benchmark's C version is based on Tcl's RE engine 
and ranks #2 on their list, far ahead of Perl/Python/PHP/Ruby.


http://benchmarksgame.alioth.debian.org/u32/program.php?test=regexdna&lang=gcc&id=1

#############################################
# notes

gcc (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3

Is this a C program or is this a Tcl program?

#############################################
# regex-dna C gcc program source code

/* The Computer Language Benchmarks Game
  * http://benchmarksgame.alioth.debian.org/
    contributed by Paul Serice
*/

#include <sys/types.h>
#include <pthread.h>
#include <errno.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <glib.h>
#include <tcl.h>

#############################################




Le 29/05/2013 11:46, Gustaf Neumann a écrit :
> Dear all.
>
> Here is a benchmark, where Tcl looks very well -- unless i
> have goofed up my
> implementation, but the output is correct. Interestingly Tcl
> 8.6 is on this test
> better than Tcl 8.5 and Perl 5.12), Python (3.3.2), PHP and
> Ruby (1.8 and 2.0).
> All tests are made on a recent Imac (2.9 GHz Intel i5 under
> Mac OS X 10.8.3).
>
> The test sources and various implementations are here:
> http://benchmarksgame.alioth.debian.org/u32/benchmark.php?test=regexdna&lang=all&id=2&data=u32
>
> The implementation is below and straightforward.
>
> -gustaf neumann
>
> ======================================================================
> Tcl 8.6
> % time tclsh ~/scripts/regex-dna.tcl < ~/scripts/regexdna-input5000000.txt
> real	0m5.295s
> user	0m4.463s
> sys	0m0.826s
>
> Tcl 8.5
> % time tclsh8.5 ~/scripts/regex-dna.tcl < ~/scripts/regexdna-input5000000.txt
> real	0m7.975s
> user	0m6.784s
> sys	0m1.180s
>
> Perl 5 (v5.12.4) regex-dna Perl #2
> % time perl  ~/scripts/regex-dna2.pl < ~/scripts/regexdna-input5000000.txt
> real	0m9.473s
> user	0m28.609s
> sys	0m0.578s
>
> Python (Python 3.3.2) regex-dna Python 3 #5
> % time python3.3  ~/scripts/regex-dna.py < ~/scripts/regexdna-input5000000.txt
> real	0m16.228s
> user	0m15.538s
> sys	0m0.671s
>
> PHP (PHP 5.3.15) regex-dna PHP #3
> % time php -n -d memory_limit=512M ~/scripts/regex-dna.php < ~/scripts/regexdna-input5000000.txt
> real	0m19.123s
> user	0m18.706s
> sys	0m0.389s
>
> Ruby (ruby 2.0.0p195) regex-dna Ruby 2.0 #2
> time ruby  ~/scripts/regex-dna.rb < ~/scripts/regexdna-input5000000.txt
> real	0m22.703s
> user	0m22.286s
> sys	0m0.398s
>
> Ruby (ruby 1.8.7) regex-dna Ruby 2.0 #2
> time ruby  ~/scripts/regex-dna.rb < ~/scripts/regexdna-input5000000.txt
> real	0m35.371s
> user	0m34.894s
> sys	0m0.483s
>
> Perl 5 (v5.12.4) regex-dna Perl #4
> % time perl  ~/scripts/regex-dna.pl < ~/scripts/regexdna-input5000000.txt
> real	0m52.197s
> user	0m51.990s
> sys	0m0.176s
>
> ======================================================================
> set content [read stdin]
> set inputLength [string length $content]
>
> regsub -all -lineanchor {^>[^\n]*$} [string tolower $content] "" content
> regsub -all {\n} $content "" content
> set contentLength [string length $content]
>
> set patterns {
>     agggtaaa|tttaccct
>     [cgt]gggtaaa|tttaccc[acg]
>     a[act]ggtaaa|tttacc[agt]t
>     ag[act]gtaaa|tttac[agt]ct
>     agg[act]taaa|ttta[agt]cct
>     aggg[acg]aaa|ttt[cgt]ccct
>     agggt[cgt]aa|tt[acg]accct
>     agggta[cgt]a|t[acg]taccct
>     agggtaa[cgt]|[acg]ttaccct
> }
> foreach pattern $patterns {
>     puts "$pattern [regexp -all $pattern $content]"
> }
> foreach {from to} {
>     b (c|g|t)
>     d (a|g|t)
>     h (a|c|t)
>     k (g|t)
>     m (a|c)
>     n (a|c|g|t)
>     r (a|g)
>     s (c|t)
>     v (a|c|g)
>     w (a|t)
>     y (c|t)
> } {
>     regsub -all $from $content $to content
> }
> puts $inputLength\n$contentLength\n[string length $content]
> ======================================================================
>
> Output
> ======================================================================
> agggtaaa|tttaccct 356
> [cgt]gggtaaa|tttaccc[acg] 1250
> a[act]ggtaaa|tttacc[agt]t 4252
> ag[act]gtaaa|tttac[agt]ct 2894
> agg[act]taaa|ttta[agt]cct 5435
> aggg[acg]aaa|ttt[cgt]ccct 1537
> agggt[cgt]aa|tt[acg]accct 1431
> agggta[cgt]a|t[acg]taccct 1608
> agggtaa[cgt]|[acg]ttaccct 2178
> 50833411
> 50000000
> 66800214
> ======================================================================
>
>
>
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