SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Java Developer eandrade Academic/Non-Profit Jobs 1 08-22-2019 04:59 AM
Picard: problem with Java? aleidenroth Bioinformatics 9 06-29-2013 08:37 PM
Execute Tophat Via Java Stiff0810 Bioinformatics 6 07-18-2011 01:53 AM
Perl/Java Developer, Bioinformatics Position @ Cofactor Genomics pmwshrn Academic/Non-Profit Jobs 0 05-24-2011 09:37 AM
Java for bioinformatics.. vani s kulkarni Bioinformatics 1 07-30-2009 11:19 AM

Reply
 
Thread Tools
Old 12-13-2012, 12:22 PM   #1
jarwulf
Junior Member
 
Location: US

Join Date: Apr 2012
Posts: 9
Default Perl vs Java or C++

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?
jarwulf is offline   Reply With Quote
Old 12-13-2012, 01:16 PM   #2
twaddlac
Member
 
Location: Pittsburgh, PA

Join Date: Feb 2011
Posts: 49
Default

will perl fork() work?

http://perldoc.perl.org/perlfork.html
twaddlac is offline   Reply With Quote
Old 12-13-2012, 01:23 PM   #3
Richard Finney
Senior Member
 
Location: bethesda

Join Date: Feb 2009
Posts: 700
Default

Check out some bechmarks. Look around here for other bechmarks:
http://shootout.alioth.debian.org/u3...re-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.

Last edited by Richard Finney; 12-13-2012 at 01:36 PM.
Richard Finney is offline   Reply With Quote
Old 12-13-2012, 05:43 PM   #4
gsgs
Senior Member
 
Location: germany

Join Date: Oct 2009
Posts: 140
Default

post the inner loop to comp.lang.asm.x86 or such
gsgs is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 02:41 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO