Yes, use flock. And strict, warnings and 3-argument open. Some sample locking code follows. Adjust according to your needs.

use strict;
use warnings;
use Fcntl ':flock';    # import LOCK_* constants

open(my $fhlock, '>', $somelockfile) or die "Error: open '$somelockfil
+e': $!";
 
# Note: process will block at this point until the lock is acquired.
flock($fhlock, LOCK_EX) or die "Error: flock '$somelockfile': $!";
 
# Lock is now held until $fhlock is closed.
# Note that even if this program crashes or is killed, $fhlock will
# be closed by the OS and the lock released.
# ...

# Release the lock simply by closing the file handle.
close $fhlock or die "Error: close '$somelockfile': $!";
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A lock that is not automatically freed on unplanned program exit and unplanned systems restart is dangerous. It creates the possibility of a situation where a lock is thought to be held but isn't.

Having to poll the lock is inefficient (to varying degree). It can also prevent fairness (i.e. one particular process could wait forever for a lock if scheduling benefits other processes).

And now you know why flock was recommended.

Use flock.

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!
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Cheers,
Darren

As discussed in Ensuring only one copy of a perl script is running at a time, be aware that this trick works on Unix (with advisory locking), but does not work on Windows (mandatory locking).

You actually don't need the latter two lines. Just having either __DATA__ or __END__ will do.

The text after the __DATA__ is required. Without it, the program will stop working as soon as a coworker tries to improve the code. :P

P1 check if "the.lock" exists -> no
P2 check if "the.lock" exists -> no
P1 create "the.lock" -> ok
P2 create "the.lock" -> ok
P1 do "more code"
P2 do "more code"
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use Fcntl qw(:flock);

open(LOCK, ">>", "lock")
        or die "Error: could not open or create lock: $!";

print "Waiting for lock...\n";
flock(LOCK, LOCK_EX)
        or die "Error: could not get lock";
print "Got lock!\n";

print "Working exclusively...\n";
sleep(10);
print "Done.\n";

print "Release lock.\n";
flock(LOCK, LOCK_UN);
print "Done.\n";

close(LOCK);
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while ($stop = 0) {

should be

while ($stop == 0) {

One work around is to put the constant on the left in comparisons. The following will throw an error:

while (0 = $stop) {

There is some more discussion in What habits do you have to avoid introducing bugs?