Dear wise Monks,
I hereby ask your wisdom regarding the following problem:
I have a perl wrapper script that receives an input file with some protein sequences (I work with Bioinformatics) and then it calls a JAVA program that needs to run on each of the sequences separately (i,e, this piece of code cannot be parallelized, not written by me and I don't know JAVA). What I was thinking to do is, since I have like a 20 core machine, I could split the big file into smaller ones, run the JAVA code in parallel and then output all results in one file (the output file that the Perl wrapper will use to show to the user).
My question therefore is, is there a straight-forward way to do this task? I am not very experienced with Perl so if you would please be patient with me I would really appreciate that.

In reply to Run a script in parallel mode by Anonymous Monk

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.