D - Bad performance of simple regular expression
hi everyone, first of all i want to say that i'm not a professional programmer - so the problem i have might be caused by my own lack of experience. Nevertheless i want to describe it, hoping that someone in this group might be able to tell me what's wrong. I am a molecular biologist and i often have to deal with larger amounts of DNA and protein sequence data (which is in principle text). I am mainly using Perl to process these DNA files, and Perl generally performs very well (regular expressions are actually the killer tool for working with DNA sequences). Unfortunately not everything in Perl is a fast as the regular expressions and so i started trying to learn a language that can be compiled to produce fast executables : C++ - and went crazy because everything is so complicated. All the ugly details that Perl takes care of for the user have to be organized manually and that really gave me the creeps. Then i learned about D and it sounded like it the solution to my problem: A compilable language that supports associative arrays, garbage collection and (most importantly for me) regular expressions! Great! I experimented a bit and actually managed to write small working programlet directly. I was delighted! But now comes the reason why i write all this: Being enthusiastic about this new nice language i started to write a module that should implement basic functions for working with the most common DNA sequence file formats. To parse these files i planned to use regular expressions. So far so good. When testing my module with a small DNA file everything seemed OK -then i tried to use it to parse a more real world-sized DNA file (~155000 characters of DNA sequence plus about the same amount of textual information) and had to find out that a simple std.regexp.split call took about 59 seconds!!! I could not believe it and wrote a little Perl script doing the same thing and it took less than 1s!! What's wrong here??? This can't really be true, can it? Is the implementation of regular expressions in the phobos library so bad or preliminary that it is so much less performant than the Perl regex engine? It's actually not usable for me like this (which is a sad think because i really like the other features of D and would like to use it). Am i making mistakes or do i simply have to wait for a better version of phobos? Any comments or suggestions would be great. cheers
Feb 05 2007
Markus <schulz alpharesearch.de> If you look at this benchnark you will see two regex programs... one is good and the other one is not. http://shootout.alioth.debian.org/debian/benchmark.php? test=regexdna&lang=all Ratio Program & Logs Full CPU Time s Memory Use KB GZip Bytes 2.0 Python 7.33 23,592 326 2.8 Scheme MzScheme 10.04 182,448 819 3.0 Ruby 10.79 31,756 307 3.2 Java JDK -server 11.65 78,204 641 3.6 Scala 12.85 76,960 647 4.2 Lisp SBCL 15.06 305,796 709 5.0 JavaScript SpiderMonkey 18.14 180,884 349 1,208 Erlang 4,342.63 79,080 606
Apr 12 2007