Here is a technique that I picked up here at the monastery a few years back, and have been using ever since: 
use Fcntl 'LOCK_EX', 'LOCK_NB';

unless (flock DATA, LOCK_EX | LOCK_NB) {
    $logger->fatal("Found duplicate script run. Stopping");
    exit;
}

__DATA__
This exists to allow the locking code at the beginning of the file to 
+work.
DO NOT REMOVE THESE LINES!

[download]
If I can find the original node, I'll update with a link to it.
Update: Found it. this node by adamk.

Cheers,
Darren

In reply to Re: Lock File by McDarren
in thread Lock File by toniax

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