Perl vs Java or C++

[jarwulf]

We have a peakcalling program for ChipSeq written in perl with a Java UI. One of the things we want to do is to speed up the program substantially so that more jobs can be done.

I have some experience with Java and C/C++ (more than perl actually) and I was considering rewriting the core programs in one of these languages. Would there be any inherent boost to speed from a decent conversion or is there no point in even bothering to do this?

[twaddlac]

will perl fork() work?

http://perldoc.perl.org/perlfork.html

[Richard Finney]

Check out some bechmarks. Look around here for other bechmarks:

http://shootout.alioth.debian.org/u32/which-programs-are-fastest.php

You are likely to see a substantial performance boost porting your code to c/c++/java from perl.

That said, breaking your data into chunks and running in as many processes as is available on your various machines might be the easiest way to solve the problem of getting the job done quickly. Run as many processes as there are are "CPU cores" on your machine.

[gsgs]

post the inner loop to comp.lang.asm.x86 or such