I'm writing a script that iteratively runs a command on many small filess and reaps the output. The commands each take 1-2 seconds to run, and for the most part, this works. However, there's one particular instance where if I use a particular input file, then waitpid() stalls.

The command itself runs fine with that particular file in bash, and I'm aware that I can use WNOHANG to prevent waitpid from causing the script itself to stop, but I'm struggling to understand why waitpid() stalls at the same file each time.

The (incomplete) section of code I'm using is:

my $cmd = "blastp -query ".$TmpDir."/".$count.".fasta -db ".$Dir."/".$
+count.".db -outfmt 6";
$pid=open3($wtr, $rdr, $err, $cmd);
waitpid($pid, 0);

[download]

In reply to waitpid stalling on one particular file by seaver

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.